1-114377599-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377599
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377599
    reference: chr 1
allele count: 3
allele frequency: 2.474308430793593e-5
allele num: 121246
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1446A>G
  hgvsp: ENSP00000432674.1:p.Ile482Met
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1868A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1827A>G
  hgvsp: ENSP00000388229.2:p.Ile609Met
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1662A>G
  hgvsp: ENSP00000435176.1:p.Ile554Met
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1827A>G
  hgvsp: ENSP00000352833.5:p.Ile609Met
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1095A>G
  hgvsp: ENSP00000439372.1:p.Ile365Met
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1105A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15323A>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 205
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1577
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2673
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18632
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 134
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 934
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21666
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 85
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 95
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3302
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9392
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 434
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 620
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 169
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 326
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 274
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1123
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4299
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 145
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11042
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ile609Met
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: South Asian
population: African
population: Latino
population: Other
population: European (Finnish)
reference allele: T
site quality: QD
site quality: BaseQRankSum
site quality: MQ
site quality: FS
site quality: DP
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD

1-114377602-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377602
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377602
    reference: chr 1
allele count: 1
allele frequency: 8.249463784853985e-6
allele num: 121220
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1865G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15326G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1659G>A
  hgvsp: ENST00000528414.1:c.1659G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1092G>A
  hgvsp: ENST00000538253.1:c.1092G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1824G>A
  hgvsp: ENST00000359785.5:c.1824G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1102G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1443G>A
  hgvsp: ENST00000525799.1:c.1443G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1824G>A
  hgvsp: ENST00000420377.2:c.1824G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 272
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 934
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 618
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21658
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 134
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2667
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9392
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 326
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 205
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 95
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 169
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1576
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18624
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 434
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3300
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11037
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 168
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1962
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Arg608Arg
num of homozygotes: 0
population: Latino
population: East Asian
population: African
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
reference allele: C
site quality: DP
site quality: QD
site quality: VQSLOD
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: FS

http://identifiers.org/exac.variant/1-114377610-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377610
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377610
    reference: chr 1
allele count: 35
allele frequency: 2.891367203634862e-4
allele num: 121050
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1816G>T
  hgvsp: ENSP00000352833.5:p.Ala606Ser
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1094G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1816G>T
  hgvsp: ENSP00000388229.2:p.Ala606Ser
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1651G>T
  hgvsp: ENSP00000435176.1:p.Ala551Ser
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15334G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1084G>T
  hgvsp: ENSP00000439372.1:p.Ala362Ser
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1435G>T
  hgvsp: ENSP00000432674.1:p.Ala479Ser
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1857G>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 207
  bin: 7.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 173
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9383
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2625
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 97
  bin: 9.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 434
  bin: 6.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 1575
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21601
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3289
  bin: 4.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 325
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 18490
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 270
  bin: 9.75e1
  variant carriers: 16
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 935
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 616
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 35
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 131
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 169
  bin: 7.75e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 747
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10983
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35283
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Ala606Ser
num of homozygotes: 0
population: East Asian
population: African
population: South Asian
population: Other
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
reference allele: C
site quality: MQ
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: VQSLOD
site quality: MQRankSum
site quality: DP
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: FS

1-114377611-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377611
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377611
    reference: chr 1
allele count: 35
allele frequency: 2.891319432970955e-4
allele num: 121052
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1093T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15335T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1815T>C
  hgvsp: ENST00000359785.5:c.1815T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1434T>C
  hgvsp: ENST00000525799.1:c.1434T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1083T>C
  hgvsp: ENST00000538253.1:c.1083T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1650T>C
  hgvsp: ENST00000528414.1:c.1650T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1815T>C
  hgvsp: ENST00000420377.2:c.1815T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1856T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 131
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 97
  bin: 9.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 18491
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 617
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 326
  bin: 6.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 174
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21597
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1575
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3287
  bin: 4.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 168
  bin: 7.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 935
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 433
  bin: 6.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2629
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 207
  bin: 7.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 9380
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 270
  bin: 9.75e1
  variant carriers: 16
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 358
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2675
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Thr605Thr
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: Other
population: South Asian
population: European (Non-Finnish)
population: East Asian
population: African
reference allele: A
site quality: MQRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: MQ
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: BaseQRankSum

1-114377618-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377618
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377618
    reference: chr 1
allele count: 1
allele frequency: 8.27841981522567e-6
allele num: 120796
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1852-3T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1811-3T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15342T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1811-3T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1089-3T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1079-3T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1430-3T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1646-3T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3278
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 205
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18308
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 526
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 298
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 324
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 165
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 254
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 131
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 95
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2587
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1570
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21464
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 935
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 615
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9351
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 430
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 747
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1111
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3077
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 108
  bin: 2.75e1
  variant carriers: 0
hgvs: c.1811-3T>C
num of homozygotes: 0
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: European (Finnish)
population: African
population: Other
population: Latino
reference allele: A
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: FS
site quality: VQSLOD
site quality: MQRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: QD
site quality: ReadPosRankSum
site quality: DP

http://identifiers.org/exac.variant/1-114377621-CA-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377621
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377620
    reference: chr 1
allele count: 5
allele frequency: 4.147794203042821e-5
allele num: 120546
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1811-7delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1852-7delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1089-7delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1430-7delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1079-7delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1811-7delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1646-7delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15346delT
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 18059
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9311
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 405
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1570
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21298
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 430
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 95
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 85
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 129
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 843
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2553
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 252
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 165
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3270
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 614
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 934
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 204
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 153
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 187
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10781
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 959
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 78
  bin: 3.75e1
  variant carriers: 0
hgvs: c.1811-7delT
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: Latino
population: African
population: East Asian
population: European (Finnish)
population: South Asian
reference allele: CA
site quality: FS
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: QD
site quality: DP
site quality: ClippingRankSum

1-114377639-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377639
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377639
    reference: chr 1
allele count: 7
allele frequency: 5.839562199679658e-5
allele num: 119872
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1811-24C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15363C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1811-24C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1852-24C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1430-24C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1089-24C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1079-24C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1646-24C>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2868
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 430
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1551
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 927
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 680
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20375
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 784
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 205
  bin: 7.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 165
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3192
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9072
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 612
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2262
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 128
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 16644
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 251
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 62
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2460
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 747
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 739
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1098
  bin: 9.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: African
population: Other
population: Latino
population: European (Non-Finnish)
population: South Asian
population: East Asian
reference allele: G
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: DP
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: BaseQRankSum
site quality: ClippingRankSum

1-114377642-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377642
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377642
    reference: chr 1
allele count: 1
allele frequency: 8.351567589236499e-6
allele num: 119738
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1079-27T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1852-27T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1811-27T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1089-27T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1430-27T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1811-27T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1646-27T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15366T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 924
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20018
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3138
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 251
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 726
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8904
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3477
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16260
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 203
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1085
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2270
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 610
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 429
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 127
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 164
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1542
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 443
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2911
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2916
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 131
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2423
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 947
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1097
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 739
  bin: 8.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: African
population: Other
population: East Asian
population: Latino
population: European (Non-Finnish)
reference allele: A
site quality: ClippingRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: MQ
site quality: QD

http://identifiers.org/exac.variant/1-114377652-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377652
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377652
    reference: chr 1
allele count: 1
allele frequency: 8.394050297149381e-6
allele num: 119132
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1430-37T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1646-37T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15376T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1852-37T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1079-37T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1811-37T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1811-37T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1089-37T>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 17367
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13550
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 171
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1867
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5260
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8103
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3023
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 251
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 127
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5723
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 430
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 900
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 163
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 608
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 203
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 921
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1530
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1835
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 266
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2624
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1092
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5299
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 369
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2797
  bin: 7.75e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: South Asian
population: African
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
reference allele: A
site quality: DP
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: FS
site quality: MQRankSum
site quality: QD

http://identifiers.org/exac.variant/1-114377659-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377659
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377659
    reference: chr 1
allele count: 1
allele frequency: 8.474145382438182e-6
allele num: 118006
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1811-44G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15383G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1811-44G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1079-44G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1852-44G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1430-44G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1089-44G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1646-44G>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1287
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13265
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7093
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5822
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 200
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5645
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10390
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2871
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1518
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 918
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 204
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 607
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 429
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 127
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9396
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 251
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 725
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1091
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6749
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1470
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1817
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1974
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 507
  bin: 7.5e0
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: East Asian
population: African
population: European (Finnish)
population: Other
population: Latino
population: European (Non-Finnish)
reference allele: C
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: FS
site quality: ClippingRankSum
site quality: DP
site quality: VQSLOD
site quality: BaseQRankSum
site quality: MQ

1-114377659-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114377659
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114377659
    reference: chr 1
allele count: 1
allele frequency: 8.474145382438182e-6
allele num: 118006
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1811-44G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1430-44G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1811-44G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1646-44G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1079-44G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1852-44G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-15383G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1089-44G>A
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 200
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13265
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 607
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 918
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 429
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7093
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1287
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5645
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5822
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10390
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1518
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 204
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 9396
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2871
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 127
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 251
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2738
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6059
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 507
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4205
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 239
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6749
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 238
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4207
  bin: 9.75e1
  variant carriers: 1
num of homozygotes: 0
population: Other
population: African
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
population: South Asian
population: Latino
reference allele: C
site quality: ReadPosRankSum
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: QD

1-114380161-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380161
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380161
    reference: chr 1
allele count: 1
allele frequency: 9.641527989355753e-6
allele num: 103718
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1810+51T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1078+51T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1429+51T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1088+51T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1810+51T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1645+51T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1851+51T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17885T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 6627
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1756
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11938
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1801
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9098
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10885
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 423
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4503
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 186
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 373
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 916
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 614
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10354
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4993
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4151
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3952
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 12743
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1310
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5170
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2298
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1498
  bin: 8.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: South Asian
population: African
population: Other
population: Latino
population: European (Non-Finnish)
reference allele: A
site quality: MQ
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: QD
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: FS
site quality: DP

1-114380171-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380171
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380171
    reference: chr 1
allele count: 1
allele frequency: 9.57450882769714e-6
allele num: 104444
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1088+41A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1851+41A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1429+41A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1810+41A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1078+41A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1810+41A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17895A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1645+41A>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8607
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6665
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 373
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1510
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 915
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5141
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4703
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11947
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 614
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1810
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 186
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16594
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 746
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 628
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2280
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1274
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3950
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1898
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3865
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20813
  bin: 6.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: African
population: South Asian
population: Other
population: European (Non-Finnish)
population: Latino
reference allele: T
site quality: BaseQRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: FS
site quality: ClippingRankSum
site quality: DP
site quality: MQRankSum
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff

1-114380175-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380175
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380175
    reference: chr 1
allele count: 101
allele frequency: 9.639244130559267e-4
allele num: 104780
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1645+37T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17899T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1851+37T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1088+37T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1429+37T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1078+37T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1810+37T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1810+37T>A
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 18370
  bin: 2.25e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 622
  bin: 4.75e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 6704
  bin: 7.5e0
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 1821
  bin: 3.75e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 426
  bin: 5.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 7826
  bin: 1.25e1
  variant carriers: 11
genotype depth: GenotypeDepth
  all individuals: 12460
  bin: 2.75e1
  variant carriers: 16
genotype depth: GenotypeDepth
  all individuals: 4778
  bin: 3.25e1
  variant carriers: 11
genotype depth: GenotypeDepth
  all individuals: 1304
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3701
  bin: 1.75e1
  variant carriers: 16
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 924
  bin: 4.25e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 373
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 142
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 186
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 139
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 634
  bin: 8.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 5370
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2165
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2853
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1152
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1026
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 508
  bin: 1.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: African
population: South Asian
population: East Asian
population: Latino
population: Other
population: European (Non-Finnish)
reference allele: A
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: QD
site quality: MQ
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: DP

1-114380185-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380185
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380185
    reference: chr 1
allele count: 1
allele frequency: 9.396200176648564e-6
allele num: 106426
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1810+27G>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1810+27G>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1645+27G>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1088+27G>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1078+27G>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1851+27G>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1429+27G>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17909G>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1412
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13557
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 142
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23017
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 782
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 373
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4951
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1845
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6365
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 617
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5062
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 921
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 425
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1271
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 245
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2123
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28565
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 450
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 404
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 164
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1611
  bin: 2.75e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: South Asian
population: East Asian
population: Latino
population: Other
population: European (Non-Finnish)
population: European (Finnish)
reference allele: C
site quality: MQ
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: ClippingRankSum

1-114380187-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380187
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380187
    reference: chr 1
allele count: 2
allele frequency: 1.86514967826168e-5
allele num: 107230
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17911T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1078+25T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1810+25T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1810+25T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1088+25T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1851+25T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1429+25T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1645+25T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 929
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1837
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24012
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 668
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13743
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6174
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 617
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 142
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4996
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1141
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 425
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4420
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 373
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 627
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1570
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 312
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 174
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 332
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3960
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 5968
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6571
  bin: 2.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: Other
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: Latino
population: South Asian
reference allele: A
site quality: VQSLOD
site quality: FS
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQRankSum
site quality: MQ
site quality: DP
site quality: ReadPosRankSum
site quality: QD

1-114380189-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380189
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380189
    reference: chr 1
allele count: 1
allele frequency: 9.271793350269808e-6
allele num: 107854
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1088+23C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1810+23C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17913C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1810+23C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1429+23C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1851+23C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1078+23C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1645+23C>A
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 5037
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5909
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 583
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24883
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 425
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1851
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 142
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 929
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 373
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 923
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3859
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13952
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 617
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6040
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 281
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 190
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 571
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 853
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1588
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 105
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2129
  bin: 7.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: South Asian
population: Latino
population: Other
population: African
population: European (Finnish)
population: East Asian
reference allele: G
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: FS
site quality: ClippingRankSum
site quality: QD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: DP

1-114380197-TA-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380197
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380196
    reference: chr 1
allele count: 1
allele frequency: 9.015181565756734e-6
allele num: 110924
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1810+14delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1429+14delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1810+14delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1078+14delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1851+14delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17922delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1088+14delT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1645+14delT
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 372
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4660
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 931
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27815
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1869
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14456
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5145
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 142
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2155
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 534
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 425
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 620
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 264
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2539
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 149
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 817
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 872
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 443
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4946
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 369
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 1.75e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: South Asian
population: African
population: European (Finnish)
population: Other
population: East Asian
population: European (Non-Finnish)
reference allele: TA
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: DP
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQ
site quality: FS
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: QD

http://identifiers.org/exac.variant/1-114380202-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380202
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380202
    reference: chr 1
allele count: 1
allele frequency: 8.883045818750333e-6
allele num: 112574
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1851+10T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1078+10T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1645+10T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1088+10T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17926T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1429+10T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1810+10T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1810+10T>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3946
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1871
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29070
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 299
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 619
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1619
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 263
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 934
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14623
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5177
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 410
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 551
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2542
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 330
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 597
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2240
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 666
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 150
  bin: 4.75e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: African
population: East Asian
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Latino
reference allele: A
site quality: QD
site quality: FS
site quality: VQSLOD
site quality: DP
site quality: MQ
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ClippingRankSum

1-114380206-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380206
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380206
    reference: chr 1
allele count: 2
allele frequency: 1.754755387099038e-5
allele num: 113976
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1088+6T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1078+6T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1810+6T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1851+6T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1429+6T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1810+6T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1645+6T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17930T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 188
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1209
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 249
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1876
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 373
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5207
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 142
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3305
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30088
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 935
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14770
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 329
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 620
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 251
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 460
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 257
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2259
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3974
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 670
  bin: 8.75e1
  variant carriers: 0
hgvs: c.1810+6T>C
num of homozygotes: 0
population: Latino
population: East Asian
population: South Asian
population: African
population: European (Non-Finnish)
population: Other
population: European (Finnish)
reference allele: A
site quality: FS
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: QD
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: MQ

1-114380229-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380229
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380229
    reference: chr 1
allele count: 1
allele frequency: 8.349196807267141e-6
allele num: 119772
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1628A>G
  hgvsp: ENSP00000435176.1:p.Gln543Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1412A>G
  hgvsp: ENSP00000432674.1:p.Gln471Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1834A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1793A>G
  hgvsp: ENSP00000352833.5:p.Gln598Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1793A>G
  hgvsp: ENSP00000388229.2:p.Gln598Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1071A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17953A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1061A>G
  hgvsp: ENSP00000439372.1:p.Gln354Arg
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 626
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 366
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 426
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1886
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5344
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 118
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 177
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 609
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 211
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 142
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 81
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15777
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32964
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 936
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 173
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 57
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 644
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3989
  bin: 9.75e1
  variant carriers: 1
hgvs: p.Gln598Arg
num of homozygotes: 0
population: East Asian
population: African
population: European (Finnish)
population: Latino
population: Other
population: South Asian
population: European (Non-Finnish)
reference allele: T
site quality: MQ
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP
site quality: QD
site quality: FS
site quality: VQSLOD

1-114380237-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380237
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380237
    reference: chr 1
allele count: 1
allele frequency: 8.321129010784183e-6
allele num: 120176
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1404A>G
  hgvsp: ENST00000525799.1:c.1404A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1785A>G
  hgvsp: ENST00000420377.2:c.1785A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1620A>G
  hgvsp: ENST00000528414.1:c.1620A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1053A>G
  hgvsp: ENST00000538253.1:c.1053A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1826A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1063A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1785A>G
  hgvsp: ENST00000359785.5:c.1785A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17961A>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 149
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5318
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15913
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 427
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 626
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 927
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 94
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 435
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 149
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 267
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 498
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 32963
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1869
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 110
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 67
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6968
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 156
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2600
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 39
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Leu595Leu
num of homozygotes: 0
population: European (Finnish)
population: Other
population: Latino
population: African
population: East Asian
population: European (Non-Finnish)
population: South Asian
reference allele: T
site quality: QD
site quality: DP
site quality: FS
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQRankSum
site quality: MQ

1-114380237-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380237
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380237
    reference: chr 1
allele count: 250
allele frequency: 2.080282252696046e-3
allele num: 120176
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17961A>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1785A>C
  hgvsp: ENST00000359785.5:c.1785A>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1063A>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1785A>C
  hgvsp: ENST00000420377.2:c.1785A>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1826A>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1053A>C
  hgvsp: ENST00000538253.1:c.1053A>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1404A>C
  hgvsp: ENST00000525799.1:c.1404A>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1620A>C
  hgvsp: ENST00000528414.1:c.1620A>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 149
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1869
  bin: 3.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 5318
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 626
  bin: 4.75e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 927
  bin: 4.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 427
  bin: 5.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 149
  bin: 7.25e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 267
  bin: 6.25e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 5.75e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 8.75e1
  variant carriers: 16
genotype depth: GenotypeDepth
  all individuals: 94
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 435
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32963
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15913
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 8.25e1
  variant carriers: 18
genotype depth: GenotypeDepth
  all individuals: 498
  bin: 9.75e1
  variant carriers: 132
genotype depth: GenotypeDepth
  all individuals: 110
  bin: 7.75e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 9.25e1
  variant carriers: 10
genotype quality: GenotypeQuality
  all individuals: 464
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4182
  bin: 9.75e1
  variant carriers: 245
genotype quality: GenotypeQuality
  all individuals: 2600
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 46
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1656
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Leu595Leu
num of homozygotes: 5
population: European (Non-Finnish)
population: European (Finnish)
population: South Asian
population: East Asian
population: Latino
population: Other
population: African
reference allele: T
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: QD
site quality: ClippingRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: MQ

1-114380241-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380241
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380241
    reference: chr 1
allele count: 25
allele frequency: 2.076929467475285e-4
allele num: 120370
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1049C>T
  hgvsp: ENSP00000439372.1:p.Ser350Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1781C>T
  hgvsp: ENSP00000352833.5:p.Ser594Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1400C>T
  hgvsp: ENSP00000432674.1:p.Ser467Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1822C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1781C>T
  hgvsp: ENSP00000388229.2:p.Ser594Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1616C>T
  hgvsp: ENSP00000435176.1:p.Ser539Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1059C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17965C>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1902
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16043
  bin: 2.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 33021
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 126
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5390
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 630
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 955
  bin: 4.25e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 263
  bin: 6.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 435
  bin: 5.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 385
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2365
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ser594Leu
num of homozygotes: 0
population: South Asian
population: African
population: Latino
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: Other
reference allele: G
site quality: VQSLOD
site quality: MQ
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: DP
site quality: FS
site quality: BaseQRankSum
site quality: ClippingRankSum

1-114380250-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380250
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380250
    reference: chr 1
allele count: 1
allele frequency: 8.294349888855711e-6
allele num: 120564
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1772A>G
  hgvsp: ENSP00000352833.5:p.Asn591Ser
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1391A>G
  hgvsp: ENSP00000432674.1:p.Asn464Ser
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1050A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1772A>G
  hgvsp: ENSP00000388229.2:p.Asn591Ser
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1040A>G
  hgvsp: ENSP00000439372.1:p.Asn347Ser
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17974A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1813A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1607A>G
  hgvsp: ENSP00000435176.1:p.Asn536Ser
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 432
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1903
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 309
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33060
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5406
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 629
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 953
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16134
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2629
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 686
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1676
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3996
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Asn591Ser
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Latino
population: African
population: Other
population: East Asian
reference allele: T
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: FS
site quality: DP
site quality: ReadPosRankSum
site quality: BaseQRankSum

1-114380253-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380253
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380253
    reference: chr 1
allele count: 1
allele frequency: 8.289674381590291e-6
allele num: 120632
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1769C>A
  hgvsp: ENSP00000388229.2:p.Thr590Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1810C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1769C>A
  hgvsp: ENSP00000352833.5:p.Thr590Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17977C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1037C>A
  hgvsp: ENSP00000439372.1:p.Thr346Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1388C>A
  hgvsp: ENSP00000432674.1:p.Thr463Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1604C>A
  hgvsp: ENSP00000435176.1:p.Thr535Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1047C>A
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 952
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 86
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 432
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16169
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33054
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 301
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1908
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 629
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5410
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 39
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 314
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 897
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Thr590Asn
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: Other
population: South Asian
population: European (Non-Finnish)
population: African
population: East Asian
reference allele: G
site quality: ReadPosRankSum
site quality: FS
site quality: BaseQRankSum
site quality: MQRankSum
site quality: QD
site quality: ClippingRankSum
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP

1-114380254-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380254
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380254
    reference: chr 1
allele count: 1
allele frequency: 8.289674381590291e-6
allele num: 120632
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1046A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1603A>G
  hgvsp: ENSP00000435176.1:p.Thr535Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1036A>G
  hgvsp: ENSP00000439372.1:p.Thr346Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1768A>G
  hgvsp: ENSP00000352833.5:p.Thr590Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1809A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1768A>G
  hgvsp: ENSP00000388229.2:p.Thr590Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17978A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1387A>G
  hgvsp: ENSP00000432674.1:p.Thr463Ala
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 5417
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 295
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 629
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16172
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 86
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33052
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1905
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 952
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 432
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 368
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 84
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1681
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2374
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Thr590Ala
num of homozygotes: 0
population: European (Finnish)
population: Other
population: Latino
population: African
population: European (Non-Finnish)
population: South Asian
population: East Asian
reference allele: T
site quality: DP
site quality: FS
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: MQ
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: QD

1-114380256-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380256
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380256
    reference: chr 1
allele count: 3
allele frequency: 2.486201581224206e-5
allele num: 120666
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1385C>T
  hgvsp: ENSP00000432674.1:p.Pro462Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1601C>T
  hgvsp: ENSP00000435176.1:p.Pro534Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1034C>T
  hgvsp: ENSP00000439372.1:p.Pro345Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1807C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17980C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1766C>T
  hgvsp: ENSP00000352833.5:p.Pro589Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1044C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1766C>T
  hgvsp: ENSP00000388229.2:p.Pro589Leu
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 432
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33067
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5415
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 370
  bin: 9.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 294
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 90
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1907
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 630
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 952
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16178
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40792
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 74
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2622
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2376
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Pro589Leu
num of homozygotes: 0
population: Latino
population: East Asian
population: Other
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: South Asian
reference allele: G
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQ
site quality: QD
site quality: DP
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: BaseQRankSum
site quality: ClippingRankSum

1-114380269-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380269
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380269
    reference: chr 1
allele count: 1
allele frequency: 8.274309922552459e-6
allele num: 120856
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1021T>A
  hgvsp: ENSP00000439372.1:p.Ser341Thr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1588T>A
  hgvsp: ENSP00000435176.1:p.Ser530Thr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1753T>A
  hgvsp: ENSP00000352833.5:p.Ser585Thr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1794T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1372T>A
  hgvsp: ENSP00000432674.1:p.Ser458Thr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1753T>A
  hgvsp: ENSP00000388229.2:p.Ser585Thr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1031T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17993T>A
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 247
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5432
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 630
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33091
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 954
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 433
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16249
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 188
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1906
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3997
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 254
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Ser585Thr
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: Latino
population: Other
population: South Asian
reference allele: A
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: DP

1-114380270-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380270
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380270
    reference: chr 1
allele count: 1
allele frequency: 8.274036074797286e-6
allele num: 120860
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1020A>C
  hgvsp: ENSP00000439372.1:p.Leu340Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1752A>C
  hgvsp: ENSP00000388229.2:p.Leu584Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-17994A>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1752A>C
  hgvsp: ENSP00000352833.5:p.Leu584Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1587A>C
  hgvsp: ENSP00000435176.1:p.Leu529Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1371A>C
  hgvsp: ENSP00000432674.1:p.Leu457Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1030A>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1793A>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1907
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 242
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 631
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5434
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 433
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16250
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33094
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 954
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3997
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 689
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Leu584Phe
num of homozygotes: 0
population: African
population: Latino
population: East Asian
population: European (Finnish)
population: Other
population: European (Non-Finnish)
population: South Asian
reference allele: T
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: MQRankSum
site quality: MQ
site quality: DP
site quality: VQSLOD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: QD

1-114380278-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380278
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380278
    reference: chr 1
allele count: 6
allele frequency: 4.959743415940615e-5
allele num: 120974
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1744G>A
  hgvsp: ENSP00000388229.2:p.Asp582Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1363G>A
  hgvsp: ENSP00000432674.1:p.Asp455Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1744G>A
  hgvsp: ENSP00000352833.5:p.Asp582Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1022G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18002G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1012G>A
  hgvsp: ENSP00000439372.1:p.Asp338Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1579G>A
  hgvsp: ENSP00000435176.1:p.Asp527Asn
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1785G>A
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 33133
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5442
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 433
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1908
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 954
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 372
  bin: 9.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 630
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16267
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 687
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2627
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2376
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Asp582Asn
num of homozygotes: 0
population: East Asian
population: African
population: South Asian
population: Other
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
reference allele: C
site quality: DP
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: BaseQRankSum
site quality: MQRankSum
site quality: FS
site quality: MQ
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: QD

1-114380279-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380279
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380279
    reference: chr 1
allele count: 1
allele frequency: 8.264326209484141e-6
allele num: 121002
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1784T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1743T>C
  hgvsp: ENST00000420377.2:c.1743T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18003T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1021T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1743T>C
  hgvsp: ENST00000359785.5:c.1743T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1578T>C
  hgvsp: ENST00000528414.1:c.1578T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1011T>C
  hgvsp: ENST00000538253.1:c.1011T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1362T>C
  hgvsp: ENST00000525799.1:c.1362T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 955
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5442
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 368
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 188
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 432
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33148
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1912
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16265
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 630
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 904
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1681
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2626
  bin: 7.75e1
  variant carriers: 0
hgvs: p.His581His
num of homozygotes: 0
population: East Asian
population: South Asian
population: Other
population: Latino
population: European (Finnish)
population: African
population: European (Non-Finnish)
reference allele: A
site quality: ReadPosRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: QD
site quality: DP
site quality: InbreedingCoeff

1-114380280-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380280
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380280
    reference: chr 1
allele count: 6
allele frequency: 4.958513768139896e-5
allele num: 121004
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1742A>G
  hgvsp: ENSP00000388229.2:p.His581Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1783A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1577A>G
  hgvsp: ENSP00000435176.1:p.His526Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1020A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1742A>G
  hgvsp: ENSP00000352833.5:p.His581Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18004A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1361A>G
  hgvsp: ENSP00000432674.1:p.His454Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1010A>G
  hgvsp: ENSP00000439372.1:p.His337Arg
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 630
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 16260
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 955
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 184
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 432
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5447
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1911
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33148
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4002
  bin: 9.75e1
  variant carriers: 6
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2626
  bin: 7.75e1
  variant carriers: 0
hgvs: p.His581Arg
num of homozygotes: 0
population: European (Finnish)
population: Other
population: South Asian
population: Latino
population: African
population: East Asian
population: European (Non-Finnish)
reference allele: T
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: FS
site quality: QD
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: DP

1-114380281-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380281
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380281
    reference: chr 1
allele count: 1
allele frequency: 8.263506701703935e-6
allele num: 121014
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18005C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1360C>T
  hgvsp: ENSP00000432674.1:p.His454Tyr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1782C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1741C>T
  hgvsp: ENSP00000388229.2:p.His581Tyr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.1009C>T
  hgvsp: ENSP00000439372.1:p.His337Tyr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1741C>T
  hgvsp: ENSP00000352833.5:p.His581Tyr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1019C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1576C>T
  hgvsp: ENSP00000435176.1:p.His526Tyr
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 956
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1911
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16268
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 181
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 632
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33143
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 432
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5447
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 189
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 902
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2627
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2372
  bin: 7.25e1
  variant carriers: 0
hgvs: p.His581Tyr
num of homozygotes: 0
population: Latino
population: East Asian
population: European (Finnish)
population: Other
population: South Asian
population: African
population: European (Non-Finnish)
reference allele: G
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: MQ
site quality: DP
site quality: QD
site quality: ReadPosRankSum
site quality: FS
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQRankSum

1-114380297-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380297
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380297
    reference: chr 1
allele count: 1
allele frequency: 8.250552787036732e-6
allele num: 121204
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1344C>T
  hgvsp: ENST00000525799.1:c.1344C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1725C>T
  hgvsp: ENST00000420377.2:c.1725C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1560C>T
  hgvsp: ENST00000528414.1:c.1560C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18021C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1725C>T
  hgvsp: ENST00000359785.5:c.1725C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.993C>T
  hgvsp: ENST00000538253.1:c.993C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1766C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1003C>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 632
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16307
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5449
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33204
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 955
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 101
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 433
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1912
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 368
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1679
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Phe575Phe
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: Latino
population: Other
population: South Asian
reference allele: G
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: BaseQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQ
site quality: FS
site quality: QD
site quality: ClippingRankSum

1-114380300-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380300
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380300
    reference: chr 1
allele count: 1
allele frequency: 8.249191579225235e-6
allele num: 121224
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1341C>T
  hgvsp: ENST00000525799.1:c.1341C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*1000C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1557C>T
  hgvsp: ENST00000528414.1:c.1557C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18024C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1722C>T
  hgvsp: ENST00000420377.2:c.1722C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.990C>T
  hgvsp: ENST00000538253.1:c.990C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1722C>T
  hgvsp: ENST00000359785.5:c.1722C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1763C>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1912
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 92
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5450
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 632
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16313
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33194
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 432
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 957
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 67
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2628
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3996
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 113
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 39
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Leu574Leu
num of homozygotes: 0
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
population: Latino
population: African
population: South Asian
population: Other
reference allele: G
site quality: ClippingRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: DP
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: QD

1-114380303-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380303
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380303
    reference: chr 1
allele count: 1
allele frequency: 8.246334504312833e-6
allele num: 121266
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.987C>T
  hgvsp: ENST00000538253.1:c.987C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1719C>T
  hgvsp: ENST00000420377.2:c.1719C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1338C>T
  hgvsp: ENST00000525799.1:c.1338C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*997C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1760C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1554C>T
  hgvsp: ENST00000528414.1:c.1554C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1719C>T
  hgvsp: ENST00000359785.5:c.1719C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18027C>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 33206
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16325
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 71
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 70
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5451
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 632
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1911
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 188
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 368
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 959
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 433
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7077
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 688
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Ser573Ser
num of homozygotes: 0
population: South Asian
population: Other
population: African
population: East Asian
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
reference allele: G
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: MQ
site quality: QD
site quality: DP

1-114380304-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380304
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380304
    reference: chr 1
allele count: 1
allele frequency: 8.245382585751979e-6
allele num: 121280
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18028C>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1553C>G
  hgvsp: ENSP00000435176.1:p.Ser518Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.986C>G
  hgvsp: ENSP00000439372.1:p.Ser329Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1718C>G
  hgvsp: ENSP00000352833.5:p.Ser573Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1759C>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1718C>G
  hgvsp: ENSP00000388229.2:p.Ser573Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*996C>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1337C>G
  hgvsp: ENSP00000432674.1:p.Ser446Cys
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 64
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5458
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 958
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 433
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33209
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16323
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1911
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 632
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 368
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2628
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7078
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1679
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2374
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Ser573Cys
num of homozygotes: 0
population: European (Finnish)
population: African
population: Latino
population: East Asian
population: European (Non-Finnish)
population: Other
population: South Asian
reference allele: G
site quality: DP
site quality: InbreedingCoeff
site quality: QD
site quality: MQ
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum

1-114380317-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380317
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380317
    reference: chr 1
allele count: 2
allele frequency: 1.648070932972955e-5
allele num: 121354
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*983A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1705A>G
  hgvsp: ENSP00000352833.5:p.Thr569Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1705A>G
  hgvsp: ENSP00000388229.2:p.Thr569Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.973A>G
  hgvsp: ENSP00000439372.1:p.Thr325Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1540A>G
  hgvsp: ENSP00000435176.1:p.Thr514Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1746A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18041A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1324A>G
  hgvsp: ENSP00000432674.1:p.Thr442Ala
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5456
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16361
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 957
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 370
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1912
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 433
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33219
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 631
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 70
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1679
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2634
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2379
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Thr569Ala
num of homozygotes: 0
population: African
population: East Asian
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
population: Latino
population: Other
reference allele: T
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQRankSum
site quality: QD
site quality: MQ
site quality: VQSLOD
site quality: FS
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP

1-114380321-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380321
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380321
    reference: chr 1
allele count: 75
allele frequency: 6.179858604835122e-4
allele num: 121362
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.969G>A
  hgvsp: ENST00000538253.1:c.969G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*979G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1701G>A
  hgvsp: ENST00000420377.2:c.1701G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1536G>A
  hgvsp: ENST00000528414.1:c.1536G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18045G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1701G>A
  hgvsp: ENST00000359785.5:c.1701G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1742G>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1320G>A
  hgvsp: ENST00000525799.1:c.1320G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 16355
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 105
  bin: 7.75e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 9.25e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 24
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1908
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 149
  bin: 7.25e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 33161
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5453
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 8.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 631
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 71
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 376
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 957
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 408
  bin: 9.75e1
  variant carriers: 40
genotype depth: GenotypeDepth
  all individuals: 87
  bin: 8.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 6.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 434
  bin: 5.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2374
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1677
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Leu567Leu
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: African
population: South Asian
population: Latino
population: European (Finnish)
population: Other
reference allele: C
site quality: VQSLOD
site quality: FS
site quality: MQ
site quality: ClippingRankSum
site quality: DP
site quality: MQRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: ReadPosRankSum

http://identifiers.org/exac.variant/1-114380322-AAC-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380322
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380320
    reference: chr 1
allele count: 1
allele frequency: 8.239947264337508e-6
allele num: 121360
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1739_1740delGT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1317_1318delGT
  hgvsp: ENSP00000432674.1:p.Leu440AlafsTer15
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.966_967delGT
  hgvsp: ENSP00000439372.1:p.Leu323AlafsTer15
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*976_*977delGT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18048_469-18047delGT
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1698_1699delGT
  hgvsp: ENSP00000388229.2:p.Leu567AlafsTer15
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1533_1534delGT
  hgvsp: ENSP00000435176.1:p.Leu512AlafsTer15
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1698_1699delGT
  hgvsp: ENSP00000352833.5:p.Leu567AlafsTer15
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: frameshift
filter: VQSRTrancheINDEL95.00to96.00
genotype depth: GenotypeDepth
  all individuals: 633
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 376
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33179
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16381
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1914
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 438
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 961
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5466
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2378
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Leu567AlafsTer15
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
population: African
population: Other
population: South Asian
reference allele: AAC
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: QD
site quality: MQ
site quality: VQSLOD
site quality: DP
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum

1-114380328-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380328
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380328
    reference: chr 1
allele count: 2
allele frequency: 1.647962294622699e-5
allele num: 121362
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1735C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.962C>T
  hgvsp: ENSP00000439372.1:p.Ser321Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1529C>T
  hgvsp: ENSP00000435176.1:p.Ser510Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1313C>T
  hgvsp: ENSP00000432674.1:p.Ser438Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1694C>T
  hgvsp: ENSP00000352833.5:p.Ser565Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1694C>T
  hgvsp: ENSP00000388229.2:p.Ser565Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18052C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*972C>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 634
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5472
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33180
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16382
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 962
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 371
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1916
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4009
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 7088
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1682
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Ser565Phe
num of homozygotes: 0
population: Latino
population: East Asian
population: European (Non-Finnish)
population: South Asian
population: Other
population: African
population: European (Finnish)
reference allele: G
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: QD
site quality: VQSLOD

1-114380332-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380332
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380332
    reference: chr 1
allele count: 3
allele frequency: 2.471658317954126e-5
allele num: 121376
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1309T>C
  hgvsp: ENSP00000432674.1:p.Ser437Pro
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.958T>C
  hgvsp: ENSP00000439372.1:p.Ser320Pro
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1731T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*968T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1525T>C
  hgvsp: ENSP00000435176.1:p.Ser509Pro
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1690T>C
  hgvsp: ENSP00000388229.2:p.Ser564Pro
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18056T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1690T>C
  hgvsp: ENSP00000352833.5:p.Ser564Pro
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16385
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1916
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 964
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 371
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33191
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5468
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 634
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2376
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1683
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Ser564Pro
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: Other
population: Latino
population: European (Finnish)
population: East Asian
population: African
reference allele: A
site quality: BaseQRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: DP
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: QD

1-114380339-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380339
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380339
    reference: chr 1
allele count: 7
allele frequency: 5.766632616074076e-5
allele num: 121388
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*961T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1683T>C
  hgvsp: ENST00000359785.5:c.1683T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1683T>C
  hgvsp: ENST00000420377.2:c.1683T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.951T>C
  hgvsp: ENST00000538253.1:c.951T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1302T>C
  hgvsp: ENST00000525799.1:c.1302T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18063T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1518T>C
  hgvsp: ENST00000528414.1:c.1518T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1724T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33193
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1917
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 964
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5471
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 635
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 372
  bin: 9.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 16393
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2377
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2627
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Val561Val
num of homozygotes: 0
population: Other
population: European (Finnish)
population: East Asian
population: South Asian
population: African
population: Latino
population: European (Non-Finnish)
reference allele: A
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: MQRankSum
site quality: FS
site quality: BaseQRankSum
site quality: QD
site quality: InbreedingCoeff

1-114380340-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380340
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380340
    reference: chr 1
allele count: 1
allele frequency: 8.238046594391538e-6
allele num: 121388
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1682T>A
  hgvsp: ENSP00000388229.2:p.Val561Asp
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1723T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1301T>A
  hgvsp: ENSP00000432674.1:p.Val434Asp
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*960T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1517T>A
  hgvsp: ENSP00000435176.1:p.Val506Asp
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.950T>A
  hgvsp: ENSP00000439372.1:p.Val317Asp
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18064T>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1682T>A
  hgvsp: ENSP00000352833.5:p.Val561Asp
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1918
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16392
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5473
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 370
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 635
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 376
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 964
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33196
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 688
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Val561Asp
num of homozygotes: 0
population: East Asian
population: South Asian
population: European (Finnish)
population: Latino
population: European (Non-Finnish)
population: African
population: Other
reference allele: A
site quality: ReadPosRankSum
site quality: QD
site quality: DP
site quality: FS
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: ClippingRankSum

1-114380360-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380360
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380360
    reference: chr 1
allele count: 1
allele frequency: 8.237503706876667e-6
allele num: 121396
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1662T>C
  hgvsp: ENST00000359785.5:c.1662T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1662T>C
  hgvsp: ENST00000420377.2:c.1662T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18084T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1497T>C
  hgvsp: ENST00000528414.1:c.1497T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1281T>C
  hgvsp: ENST00000525799.1:c.1281T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.930T>C
  hgvsp: ENST00000538253.1:c.930T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1703T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*940T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1919
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 964
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33217
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16398
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5472
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 370
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 635
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7101
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2629
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Pro554Pro
num of homozygotes: 0
population: South Asian
population: African
population: Latino
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
reference allele: A
site quality: FS
site quality: MQ
site quality: InbreedingCoeff
site quality: QD
site quality: DP
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: ReadPosRankSum

1-114380386-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380386
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380386
    reference: chr 1
allele count: 6
allele frequency: 4.942013705851344e-5
allele num: 121408
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1636A>T
  hgvsp: ENSP00000388229.2:p.Ser546Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1255A>T
  hgvsp: ENSP00000432674.1:p.Ser419Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*914A>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.904A>T
  hgvsp: ENSP00000439372.1:p.Ser302Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1677A>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1471A>T
  hgvsp: ENSP00000435176.1:p.Ser491Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1636A>T
  hgvsp: ENSP00000352833.5:p.Ser546Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18110A>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1915
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 964
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33215
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 441
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16412
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5476
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 635
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 373
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 907
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2379
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Ser546Cys
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: Latino
population: East Asian
population: African
population: European (Non-Finnish)
population: Other
reference allele: T
site quality: InbreedingCoeff
site quality: FS
site quality: MQ
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: QD
site quality: BaseQRankSum
site quality: DP
site quality: ClippingRankSum

http://identifiers.org/exac.variant/1-114380391-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380391
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380391
    reference: chr 1
allele count: 1
allele frequency: 8.236689509752241e-6
allele num: 121408
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*909G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.899G>T
  hgvsp: ENSP00000439372.1:p.Gly300Val
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18115G>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1466G>T
  hgvsp: ENSP00000435176.1:p.Gly489Val
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1631G>T
  hgvsp: ENSP00000352833.5:p.Gly544Val
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1250G>T
  hgvsp: ENSP00000432674.1:p.Gly417Val
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1631G>T
  hgvsp: ENSP00000388229.2:p.Gly544Val
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1672G>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 16420
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33209
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 964
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 635
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1917
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 370
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5482
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2632
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41264
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1685
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4006
  bin: 9.75e1
  variant carriers: 1
hgvs: p.Gly544Val
num of homozygotes: 0
population: East Asian
population: South Asian
population: European (Finnish)
population: African
population: Latino
population: European (Non-Finnish)
population: Other
reference allele: C
site quality: MQRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: VQSLOD
site quality: ClippingRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: DP
site quality: FS
site quality: ReadPosRankSum

1-114380395-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380395
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380395
    reference: chr 1
allele count: 1
allele frequency: 8.236825198095647e-6
allele num: 121406
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1246A>T
  hgvsp: ENSP00000432674.1:p.Ser416Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1627A>T
  hgvsp: ENSP00000352833.5:p.Ser543Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1462A>T
  hgvsp: ENSP00000435176.1:p.Ser488Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1627A>T
  hgvsp: ENSP00000388229.2:p.Ser543Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18119A>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.895A>T
  hgvsp: ENSP00000439372.1:p.Ser299Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1668A>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*905A>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 86
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33157
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1916
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 963
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 634
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5473
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16398
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 436
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 684
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Ser543Cys
num of homozygotes: 0
population: Latino
population: Other
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
population: African
population: South Asian
reference allele: T
site quality: DP
site quality: VQSLOD
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: BaseQRankSum
site quality: QD
site quality: ClippingRankSum

1-114380395-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380395
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380395
    reference: chr 1
allele count: 98
allele frequency: 8.072088694133733e-4
allele num: 121406
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18119A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*905A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1627A>G
  hgvsp: ENSP00000388229.2:p.Ser543Gly
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1668A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1462A>G
  hgvsp: ENSP00000435176.1:p.Ser488Gly
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.895A>G
  hgvsp: ENSP00000439372.1:p.Ser299Gly
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1627A>G
  hgvsp: ENSP00000352833.5:p.Ser543Gly
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1246A>G
  hgvsp: ENSP00000432674.1:p.Ser416Gly
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 634
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1916
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 16398
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 436
  bin: 9.75e1
  variant carriers: 68
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 8.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 963
  bin: 4.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 9.25e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33157
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5473
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 86
  bin: 8.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 2627
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1683
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 684
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ser543Gly
num of homozygotes: 1
population: European (Finnish)
population: African
population: Other
population: European (Non-Finnish)
population: East Asian
population: Latino
population: South Asian
reference allele: T
site quality: DP
site quality: MQRankSum
site quality: MQ
site quality: QD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: FS
site quality: VQSLOD

1-114380396-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380396
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380396
    reference: chr 1
allele count: 1
allele frequency: 8.236825198095647e-6
allele num: 121406
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*904A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1667A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1626A>G
  hgvsp: ENST00000420377.2:c.1626A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.894A>G
  hgvsp: ENST00000538253.1:c.894A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1245A>G
  hgvsp: ENST00000525799.1:c.1245A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1461A>G
  hgvsp: ENST00000528414.1:c.1461A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1626A>G
  hgvsp: ENST00000359785.5:c.1626A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18120A>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 966
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 638
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16430
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1925
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33166
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5492
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 371
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7101
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2376
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Pro542Pro
num of homozygotes: 0
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: European (Finnish)
population: Latino
population: Other
population: African
reference allele: T
site quality: VQSLOD
site quality: MQ
site quality: FS
site quality: MQRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: DP
site quality: ClippingRankSum

1-114380397-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380397
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380397
    reference: chr 1
allele count: 1
allele frequency: 8.236825198095647e-6
allele num: 121406
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18121C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*903C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.893C>T
  hgvsp: ENSP00000439372.1:p.Pro298Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1625C>T
  hgvsp: ENSP00000352833.5:p.Pro542Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1460C>T
  hgvsp: ENSP00000435176.1:p.Pro487Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1625C>T
  hgvsp: ENSP00000388229.2:p.Pro542Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1244C>T
  hgvsp: ENSP00000432674.1:p.Pro415Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1666C>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1924
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 966
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 638
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16433
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5491
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33165
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 371
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1688
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2636
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 904
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 689
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Pro542Leu
num of homozygotes: 0
population: African
population: European (Finnish)
population: Latino
population: East Asian
population: South Asian
population: European (Non-Finnish)
population: Other
reference allele: G
site quality: BaseQRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: DP

1-114380404-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380404
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380404
    reference: chr 1
allele count: 2
allele frequency: 1.647365039619129e-5
allele num: 121406
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18128T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1618T>C
  hgvsp: ENSP00000388229.2:p.Trp540Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1659T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1618T>C
  hgvsp: ENSP00000352833.5:p.Trp540Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.886T>C
  hgvsp: ENSP00000439372.1:p.Trp296Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1453T>C
  hgvsp: ENSP00000435176.1:p.Trp485Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1237T>C
  hgvsp: ENSP00000432674.1:p.Trp413Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*896T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33163
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5491
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16440
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1924
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 638
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 965
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 370
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2377
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1689
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 689
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2636
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7103
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Trp540Arg
num of homozygotes: 0
population: African
population: Other
population: European (Non-Finnish)
population: South Asian
population: Latino
population: European (Finnish)
population: East Asian
reference allele: A
site quality: MQRankSum
site quality: QD
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: MQ
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP

1-114380406-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380406
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380406
    reference: chr 1
allele count: 1
allele frequency: 8.236960890909689e-6
allele num: 121404
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.884C>T
  hgvsp: ENSP00000439372.1:p.Ser295Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1657C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*894C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1616C>T
  hgvsp: ENSP00000388229.2:p.Ser539Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1616C>T
  hgvsp: ENSP00000352833.5:p.Ser539Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1235C>T
  hgvsp: ENSP00000432674.1:p.Ser412Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1451C>T
  hgvsp: ENSP00000435176.1:p.Ser484Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18130C>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33163
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 638
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 965
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16443
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5491
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1924
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 371
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4017
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 689
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2635
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Ser539Leu
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: South Asian
population: Latino
population: Other
population: East Asian
reference allele: G
site quality: ReadPosRankSum
site quality: MQ
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: ClippingRankSum
site quality: DP
site quality: BaseQRankSum

1-114380407-AT-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380407
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380406
    reference: chr 1
allele count: 2
allele frequency: 1.647392178181938e-5
allele num: 121404
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.882delA
  hgvsp: ENSP00000439372.1:p.Ser295HisfsTer48
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1449delA
  hgvsp: ENSP00000435176.1:p.Ser484HisfsTer48
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1614delA
  hgvsp: ENSP00000388229.2:p.Ser539HisfsTer48
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1614delA
  hgvsp: ENSP00000352833.5:p.Ser539HisfsTer48
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18132delA
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1655delA
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*892delA
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1233delA
  hgvsp: ENSP00000432674.1:p.Ser412HisfsTer48
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5492
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 965
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 371
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33167
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 639
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1924
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16439
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2376
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4018
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 689
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Ser539HisfsTer48
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: Other
population: East Asian
population: African
population: South Asian
reference allele: AT
site quality: MQ
site quality: DP
site quality: InbreedingCoeff
site quality: QD
site quality: ClippingRankSum
site quality: FS
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: BaseQRankSum

1-114380408-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380408
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380408
    reference: chr 1
allele count: 1
allele frequency: 8.237232289950576e-6
allele num: 121400
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18132A>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1449A>T
  hgvsp: ENST00000528414.1:c.1449A>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1614A>T
  hgvsp: ENST00000359785.5:c.1614A>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*892A>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1614A>T
  hgvsp: ENST00000420377.2:c.1614A>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1233A>T
  hgvsp: ENST00000525799.1:c.1233A>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.882A>T
  hgvsp: ENST00000538253.1:c.882A>T(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1655A>T
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33166
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1924
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 370
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 638
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16438
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5493
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 965
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 689
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41253
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7102
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Ser538Ser
num of homozygotes: 0
population: South Asian
population: Latino
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: East Asian
population: Other
reference allele: T
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: QD
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum

1-114380409-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380409
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380409
    reference: chr 1
allele count: 1
allele frequency: 8.237232289950576e-6
allele num: 121400
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18133C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1613C>T
  hgvsp: ENSP00000352833.5:p.Ser538Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1232C>T
  hgvsp: ENSP00000432674.1:p.Ser411Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1613C>T
  hgvsp: ENSP00000388229.2:p.Ser538Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1654C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*891C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.881C>T
  hgvsp: ENSP00000439372.1:p.Ser294Leu
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1448C>T
  hgvsp: ENSP00000435176.1:p.Ser483Leu
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 33164
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 372
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 965
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5494
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 639
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16438
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1925
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 903
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2375
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Ser538Leu
num of homozygotes: 0
population: East Asian
population: Other
population: Latino
population: European (Finnish)
population: African
population: South Asian
population: European (Non-Finnish)
reference allele: G
site quality: BaseQRankSum
site quality: MQRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: DP
site quality: VQSLOD
site quality: FS
site quality: QD
site quality: InbreedingCoeff
site quality: ReadPosRankSum

1-114380410-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380410
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380410
    reference: chr 1
allele count: 2
allele frequency: 1.647392178181938e-5
allele num: 121404
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.880T>C
  hgvsp: ENSP00000439372.1:p.Ser294Pro
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1447T>C
  hgvsp: ENSP00000435176.1:p.Ser483Pro
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1653T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18134T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1612T>C
  hgvsp: ENSP00000352833.5:p.Ser538Pro
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1231T>C
  hgvsp: ENSP00000432674.1:p.Ser411Pro
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1612T>C
  hgvsp: ENSP00000388229.2:p.Ser538Pro
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*890T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33167
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 965
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5491
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16439
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1926
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 371
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 639
  bin: 4.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1688
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2638
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2375
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Ser538Pro
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: East Asian
population: Latino
population: South Asian
population: Other
population: European (Finnish)
reference allele: A
site quality: FS
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: MQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: DP
site quality: QD

http://identifiers.org/exac.variant/1-114380414-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380414
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380414
    reference: chr 1
allele count: 1
allele frequency: 8.236960890909689e-6
allele num: 121404
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1608T>G
  hgvsp: ENSP00000388229.2:p.Tyr536Ter
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18138T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1649T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.876T>G
  hgvsp: ENSP00000439372.1:p.Tyr292Ter
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: stop_gained
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1608T>G
  hgvsp: ENSP00000352833.5:p.Tyr536Ter
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1443T>G
  hgvsp: ENSP00000435176.1:p.Tyr481Ter
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1227T>G
  hgvsp: ENSP00000432674.1:p.Tyr409Ter
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*886T>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: stop gained
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 16439
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 638
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 965
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5493
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33170
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 376
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1923
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 370
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1689
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Tyr536Ter
num of homozygotes: 0
population: South Asian
population: Latino
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: Other
population: East Asian
reference allele: A
site quality: ClippingRankSum
site quality: FS
site quality: DP
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQ
site quality: MQRankSum
site quality: QD
site quality: VQSLOD
site quality: BaseQRankSum

1-114380424-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380424
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380424
    reference: chr 1
allele count: 1
allele frequency: 8.236825198095647e-6
allele num: 121406
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1598A>G
  hgvsp: ENSP00000352833.5:p.Glu533Gly
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1217A>G
  hgvsp: ENSP00000432674.1:p.Glu406Gly
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.866A>G
  hgvsp: ENSP00000439372.1:p.Glu289Gly
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1598A>G
  hgvsp: ENSP00000388229.2:p.Glu533Gly
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18148A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1639A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1433A>G
  hgvsp: ENSP00000435176.1:p.Glu478Gly
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*876A>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 966
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5492
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1926
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16442
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 639
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33168
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 370
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41267
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Glu533Gly
num of homozygotes: 0
population: African
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: Other
reference allele: T
site quality: MQRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: QD
site quality: DP
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: FS
site quality: ReadPosRankSum
site quality: ClippingRankSum

1-114380433-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380433
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380433
    reference: chr 1
allele count: 1
allele frequency: 8.237367996177861e-6
allele num: 121398
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*867C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1208C>A
  hgvsp: ENSP00000432674.1:p.Pro403His
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.857C>A
  hgvsp: ENSP00000439372.1:p.Pro286His
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1589C>A
  hgvsp: ENSP00000388229.2:p.Pro530His
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1589C>A
  hgvsp: ENSP00000352833.5:p.Pro530His
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1424C>A
  hgvsp: ENSP00000435176.1:p.Pro475His
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18157C>A
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1630C>A
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16436
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1927
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 967
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33164
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5492
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 642
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 371
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2372
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1685
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41260
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Pro530His
num of homozygotes: 0
population: European (Finnish)
population: Other
population: East Asian
population: Latino
population: European (Non-Finnish)
population: African
population: South Asian
reference allele: G
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD
site quality: DP

1-114380439-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380439
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380439
    reference: chr 1
allele count: 18
allele frequency: 1.482652960363744e-4
allele num: 121404
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*861A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1624A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1202A>G
  hgvsp: ENSP00000432674.1:p.Tyr401Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18163A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.851A>G
  hgvsp: ENSP00000439372.1:p.Tyr284Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1583A>G
  hgvsp: ENSP00000388229.2:p.Tyr528Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1583A>G
  hgvsp: ENSP00000352833.5:p.Tyr528Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1418A>G
  hgvsp: ENSP00000435176.1:p.Tyr473Cys
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 968
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 8.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 1925
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5495
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16440
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33143
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 640
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 85
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 379
  bin: 9.75e1
  variant carriers: 9
genotype quality: GenotypeQuality
  all individuals: 4034
  bin: 9.75e1
  variant carriers: 18
genotype quality: GenotypeQuality
  all individuals: 1685
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2630
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Tyr528Cys
num of homozygotes: 0
population: East Asian
population: Other
population: African
population: European (Non-Finnish)
population: Latino
population: South Asian
population: European (Finnish)
reference allele: T
site quality: DP
site quality: FS
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: VQSLOD
site quality: MQ
site quality: ClippingRankSum

1-114380451-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380451
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380451
    reference: chr 1
allele count: 149
allele frequency: 1.227286954516251e-3
allele num: 121406
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1406G>C
  hgvsp: ENSP00000435176.1:p.Gly469Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18175G>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1571G>C
  hgvsp: ENSP00000352833.5:p.Gly524Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1190G>C
  hgvsp: ENSP00000432674.1:p.Gly397Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1612G>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1571G>C
  hgvsp: ENSP00000388229.2:p.Gly524Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.839G>C
  hgvsp: ENSP00000439372.1:p.Gly280Ala
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*849G>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 33058
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 204
  bin: 6.75e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 266
  bin: 6.25e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 5473
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 378
  bin: 5.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 1927
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 152
  bin: 7.25e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 639
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 443
  bin: 5.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 964
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 90
  bin: 8.25e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 8.75e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 431
  bin: 9.75e1
  variant carriers: 61
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 7.75e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 9.25e1
  variant carriers: 15
genotype depth: GenotypeDepth
  all individuals: 16426
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4157
  bin: 9.75e1
  variant carriers: 146
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2622
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Gly524Ala
num of homozygotes: 3
population: Other
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: Latino
reference allele: C
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: DP
site quality: QD

http://identifiers.org/exac.variant/1-114380459-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380459
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380459
    reference: chr 1
allele count: 1
allele frequency: 8.236960890909689e-6
allele num: 121404
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1398T>G
  hgvsp: ENSP00000435176.1:p.Ser466Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.831T>G
  hgvsp: ENSP00000439372.1:p.Ser277Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1604T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1182T>G
  hgvsp: ENSP00000432674.1:p.Ser394Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18183T>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1563T>G
  hgvsp: ENSP00000352833.5:p.Ser521Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1563T>G
  hgvsp: ENSP00000388229.2:p.Ser521Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*841T>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 969
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16492
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 643
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1941
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5503
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33071
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 376
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41245
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7119
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1681
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4033
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2376
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Ser521Arg
num of homozygotes: 0
population: Other
population: African
population: European (Finnish)
population: South Asian
population: East Asian
population: Latino
population: European (Non-Finnish)
reference allele: A
site quality: VQSLOD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: QD
site quality: FS
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: DP

1-114380463-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380463
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380463
    reference: chr 1
allele count: 1
allele frequency: 8.236960890909689e-6
allele num: 121404
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18187C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1394C>T
  hgvsp: ENSP00000435176.1:p.Ser465Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1600C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.827C>T
  hgvsp: ENSP00000439372.1:p.Ser276Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*837C>T
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1559C>T
  hgvsp: ENSP00000352833.5:p.Ser520Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1178C>T
  hgvsp: ENSP00000432674.1:p.Ser393Phe
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1559C>T
  hgvsp: ENSP00000388229.2:p.Ser520Phe
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5502
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 970
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16493
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33070
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 643
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1940
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1680
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Ser520Phe
num of homozygotes: 0
population: East Asian
population: Other
population: African
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Latino
reference allele: G
site quality: BaseQRankSum
site quality: DP
site quality: FS
site quality: MQRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: ClippingRankSum
site quality: InbreedingCoeff

1-114380463-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380463
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380463
    reference: chr 1
allele count: 3
allele frequency: 2.471088267272907e-5
allele num: 121404
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1600C>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*837C>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.827C>G
  hgvsp: ENSP00000439372.1:p.Ser276Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1394C>G
  hgvsp: ENSP00000435176.1:p.Ser465Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1559C>G
  hgvsp: ENSP00000388229.2:p.Ser520Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18187C>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1559C>G
  hgvsp: ENSP00000352833.5:p.Ser520Cys
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1178C>G
  hgvsp: ENSP00000432674.1:p.Ser393Cys
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5502
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 643
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 970
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1940
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16493
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33070
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2376
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 901
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 687
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Ser520Cys
num of homozygotes: 0
population: Other
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
population: South Asian
population: East Asian
reference allele: G
site quality: DP
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: QD
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: VQSLOD
site quality: BaseQRankSum

1-114380469-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380469
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380469
    reference: chr 1
allele count: 5
allele frequency: 4.118548294097296e-5
allele num: 121402
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*831A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1172A>G
  hgvsp: ENSP00000432674.1:p.His391Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.821A>G
  hgvsp: ENSP00000439372.1:p.His274Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1553A>G
  hgvsp: ENSP00000388229.2:p.His518Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1388A>G
  hgvsp: ENSP00000435176.1:p.His463Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1594A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1553A>G
  hgvsp: ENSP00000352833.5:p.His518Arg
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18193A>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 643
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16495
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5502
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1941
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 101
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 33069
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 969
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 9.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1680
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2635
  bin: 7.75e1
  variant carriers: 0
hgvs: p.His518Arg
num of homozygotes: 0
population: Other
population: Latino
population: South Asian
population: East Asian
population: African
population: European (Non-Finnish)
population: European (Finnish)
reference allele: T
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: VQSLOD
site quality: DP
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: FS
site quality: MQ

1-114380480-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380480
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380480
    reference: chr 1
allele count: 1
allele frequency: 8.237096588194593e-6
allele num: 121402
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1542T>C
  hgvsp: ENST00000359785.5:c.1542T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1377T>C
  hgvsp: ENST00000528414.1:c.1377T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1542T>C
  hgvsp: ENST00000420377.2:c.1542T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*820T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1583T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18204T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.810T>C
  hgvsp: ENST00000538253.1:c.810T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1161T>C
  hgvsp: ENST00000525799.1:c.1161T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 33069
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1940
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 971
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16497
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5499
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 644
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4033
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41244
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2634
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Asn514Asn
num of homozygotes: 0
population: East Asian
population: Other
population: South Asian
population: African
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
reference allele: A
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: FS
site quality: ReadPosRankSum
site quality: DP
site quality: VQSLOD
site quality: QD

1-114380481-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380481
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380481
    reference: chr 1
allele count: 1
allele frequency: 8.236825198095647e-6
allele num: 121406
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.809A>C
  hgvsp: ENSP00000439372.1:p.Asn270Thr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1541A>C
  hgvsp: ENSP00000352833.5:p.Asn514Thr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1160A>C
  hgvsp: ENSP00000432674.1:p.Asn387Thr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18205A>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1582A>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1541A>C
  hgvsp: ENSP00000388229.2:p.Asn514Thr
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*819A>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1376A>C
  hgvsp: ENSP00000435176.1:p.Asn459Thr
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 971
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16496
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33068
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1941
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5500
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 644
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41244
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Asn514Thr
num of homozygotes: 0
population: East Asian
population: Latino
population: Other
population: South Asian
population: European (Finnish)
population: African
population: European (Non-Finnish)
reference allele: T
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: QD
site quality: BaseQRankSum
site quality: MQ
site quality: FS
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP

1-114380491-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380491
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380491
    reference: chr 1
allele count: 1
allele frequency: 8.236825198095647e-6
allele num: 121406
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*809A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1572A>G
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1150A>G
  hgvsp: ENSP00000432674.1:p.Asn384Asp
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1531A>G
  hgvsp: ENSP00000388229.2:p.Asn511Asp
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.799A>G
  hgvsp: ENSP00000439372.1:p.Asn267Asp
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1366A>G
  hgvsp: ENSP00000435176.1:p.Asn456Asp
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1531A>G
  hgvsp: ENSP00000352833.5:p.Asn511Asp
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18215A>G
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1941
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 375
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33072
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16493
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5499
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 971
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 644
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1681
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 688
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7115
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Asn511Asp
num of homozygotes: 0
population: South Asian
population: East Asian
population: African
population: European (Finnish)
population: Other
population: Latino
population: European (Non-Finnish)
reference allele: T
site quality: FS
site quality: DP
site quality: MQ
site quality: InbreedingCoeff
site quality: QD
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum

1-114380492-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 114380492
    reference: chr 1
  end: Position
    type: ExactPosition
    position: 114380492
    reference: chr 1
allele count: 2
allele frequency: 1.647365039619129e-5
allele num: 121406
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000439372
  ensembl transcript: ENST00000538253
  gene symbol: PTPN22
  hgvsc: ENST00000538253.1:c.798T>C
  hgvsp: ENST00000538253.1:c.798T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000134242
  ensembl transcript: ENST00000484147
  gene symbol: PTPN22
  hgvsc: ENST00000484147.1:n.1571T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000388229
  ensembl transcript: ENST00000420377
  gene symbol: PTPN22
  hgvsc: ENST00000420377.2:c.1530T>C
  hgvsp: ENST00000420377.2:c.1530T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000432674
  ensembl transcript: ENST00000525799
  gene symbol: PTPN22
  hgvsc: ENST00000525799.1:c.1149T>C
  hgvsp: ENST00000525799.1:c.1149T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000435176
  ensembl transcript: ENST00000528414
  gene symbol: PTPN22
  hgvsc: ENST00000528414.1:c.1365T>C
  hgvsp: ENST00000528414.1:c.1365T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000352833
  ensembl transcript: ENST00000359785
  gene symbol: PTPN22
  hgvsc: ENST00000359785.5:c.1530T>C
  hgvsp: ENST00000359785.5:c.1530T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000431249
  ensembl transcript: ENST00000532224
  gene symbol: PTPN22
  hgvsc: ENST00000532224.1:c.*808T>C
  variant of: http://identifiers.org/hgnc/9652
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000134242
  ensembl protein: ENSP00000433141
  ensembl transcript: ENST00000460620
  gene symbol: PTPN22
  hgvsc: ENST00000460620.1:c.469-18216T>C
  variant of: http://identifiers.org/hgnc/9652
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1941
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 101
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 644
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 971
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 6.25e1
  variant carriers: 1
hgvs: p.Arg510Arg
num of homozygotes: 0
reference allele: A

GenotypeQuality
all individuals: 1962
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 35491
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2702
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 7
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3112
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 750
bin: 8.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.000660145231951e-5
allele num: 66652
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.062075654704171e-5
allele num: 16496
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10358
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11568
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.502e1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.88e0

MQ
type: SiteQuality
SIO_000300: 5.97e1

FS
type: SiteQuality
SIO_000300: 9.879e0

DP
type: SiteQuality
SIO_000300: 2.03937e6

ClippingRankSum
type: SiteQuality
SIO_000300: 3.16e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.72e-1

MQRankSum
type: SiteQuality
SIO_000300: 6.59e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

VQSLOD
type: SiteQuality
SIO_000300: -5.581e-1

GenotypeQuality
all individuals: 2
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2702
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 35475
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3113
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 749
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1122
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4295
bin: 9.75e1
variant carriers: 1

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11568
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10352
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.500600240096038e-5
allele num: 66640
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16490
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 2.038546e6

QD
type: SiteQuality
SIO_000300: 1.87e1

VQSLOD
type: SiteQuality
SIO_000300: -4.544e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.2e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.21e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

MQ
type: SiteQuality
SIO_000300: 5.971e1

MQRankSum
type: SiteQuality
SIO_000300: 8.53e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.452e0

FS
type: SiteQuality
SIO_000300: 2.853e0

GenotypeQuality
all individuals: 1
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1953
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 44
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 28
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 6
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 4292
bin: 9.75e1
variant carriers: 35

GenotypeQuality
all individuals: 29
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1115
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3097
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2677
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 353
bin: 2.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8646
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10316
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16452
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 34
allele frequency: 5.108173076923077e-4
allele num: 66560
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.653513326410523e-5
allele num: 11556
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.962e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.82e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.84e-1

QD
type: SiteQuality
SIO_000300: 1.814e1

VQSLOD
type: SiteQuality
SIO_000300: 3.95e0

MQRankSum
type: SiteQuality
SIO_000300: 6.5e-2

DP
type: SiteQuality
SIO_000300: 2.033789e6

BaseQRankSum
type: SiteQuality
SIO_000300: -3.713e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.0e-4

FS
type: SiteQuality
SIO_000300: 0.0e0

GenotypeQuality
all individuals: 0
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4291
bin: 9.75e1
variant carriers: 35

GenotypeQuality
all individuals: 48
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1953
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 35310
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1115
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 10982
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3096
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 747
bin: 8.75e1
variant carriers: 0

Latino
type: Population
allele count: 1
allele frequency: 8.653513326410523e-5
allele num: 11556
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16452
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 34
allele frequency: 5.108019590757489e-4
allele num: 66562
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8646
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10316
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 1.19e-1

QD
type: SiteQuality
SIO_000300: 1.843e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.0e-4

VQSLOD
type: SiteQuality
SIO_000300: 3.37e0

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 2.033582e6

MQ
type: SiteQuality
SIO_000300: 5.962e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.43e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.39e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 8.78e-1

GenotypeQuality
all individuals: 18
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 7
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 3
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 34983
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4253
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 1952
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 660
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 10943
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 90
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2661
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 23
bin: 5.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66462
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.119951040391677e-5
allele num: 16340
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8640
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10286
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11550
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -5.44e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: 6.04e-1

MQRankSum
type: SiteQuality
SIO_000300: 8.37e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.43e0

MQ
type: SiteQuality
SIO_000300: 5.94e1

QD
type: SiteQuality
SIO_000300: 1.515e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.51e-1

DP
type: SiteQuality
SIO_000300: 2.023436e6

GenotypeQuality
all individuals: 25
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4244
bin: 9.75e1
variant carriers: 5

GenotypeQuality
all individuals: 8
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 744
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 19
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 85
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2634
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1944
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 34546
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 159
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3059
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1109
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 90
bin: 5.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66366
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11544
num of homozygotes: 0

African
type: Population
allele count: 5
allele frequency: 4.879953152449736e-4
allele num: 10246
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8642
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16232
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 2.236e0

MQRankSum
type: SiteQuality
SIO_000300: 8.999999999999999e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.3e-2

VQSLOD
type: SiteQuality
SIO_000300: 3.53e0

BaseQRankSum
type: SiteQuality
SIO_000300: 9.1e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

MQ
type: SiteQuality
SIO_000300: 5.986e1

QD
type: SiteQuality
SIO_000300: 1.285e1

DP
type: SiteQuality
SIO_000300: 2.014004e6

ClippingRankSum
type: SiteQuality
SIO_000300: 1.0e-2

GenotypeQuality
all individuals: 78
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 10061
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4228
bin: 9.75e1
variant carriers: 7

GenotypeQuality
all individuals: 87
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 338
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 101
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 638
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2478
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2934
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 55
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1883
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 32667
bin: 6.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10150
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 900
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11526
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 7
allele frequency: 1.059674831208938e-4
allele num: 66058
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16006
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8620
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.27e-1

MQ
type: SiteQuality
SIO_000300: 5.968e1

VQSLOD
type: SiteQuality
SIO_000300: 3.96e-1

DP
type: SiteQuality
SIO_000300: 1.963038e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.9e-3

MQRankSum
type: SiteQuality
SIO_000300: -7.01e-1

FS
type: SiteQuality
SIO_000300: 6.778e0

QD
type: SiteQuality
SIO_000300: 1.323e1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.357e0

ClippingRankSum
type: SiteQuality
SIO_000300: -7.000000000000001e-2

GenotypeQuality
all individuals: 28
bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 8.25e1
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GenotypeQuality
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bin: 2.5e0
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GenotypeQuality
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bin: 7.5e0
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GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 4222
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 778
bin: 2.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15972
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10130
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8606
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11522
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.515151515151515e-5
allele num: 66000
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.13e0

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.15e-1

VQSLOD
type: SiteQuality
SIO_000300: 3.39e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.54e0

MQRankSum
type: SiteQuality
SIO_000300: -1.128e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.0e-3

DP
type: SiteQuality
SIO_000300: 1.944693e6

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.348e1

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

GenotypeQuality
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bin: 2.5e0
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 139
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variant carriers: 0

GenotypeQuality
all individuals: 4214
bin: 9.75e1
variant carriers: 1

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15814
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9988
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.697164724299878e-5
allele num: 11498
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65748
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8584
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.841352e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.8e-3

BaseQRankSum
type: SiteQuality
SIO_000300: 4.56e0

MQ
type: SiteQuality
SIO_000300: 5.958e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.16e0

ClippingRankSum
type: SiteQuality
SIO_000300: -5.16e-1

VQSLOD
type: SiteQuality
SIO_000300: 9.17e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 1.94e-1

QD
type: SiteQuality
SIO_000300: 1.805e1

GenotypeQuality
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bin: 7.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 4.75e1
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GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15554
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.172332942555686e-4
allele num: 8530
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9780
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 880
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11458
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65198
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.7e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.7e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.9e-3

QD
type: SiteQuality
SIO_000300: 6.23e0

FS
type: SiteQuality
SIO_000300: 5.03e0

ClippingRankSum
type: SiteQuality
SIO_000300: 8.3e-2

DP
type: SiteQuality
SIO_000300: 1.729288e6

VQSLOD
type: SiteQuality
SIO_000300: -1.429e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.742e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 5234
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 344
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1974
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variant carriers: 0

GenotypeQuality
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bin: 4.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 725
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GenotypeQuality
all individuals: 86
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variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 880
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9780
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8530
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.533789380042332e-5
allele num: 65198
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15554
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11458
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.7e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 2.7e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.429e0

FS
type: SiteQuality
SIO_000300: 5.03e0

DP
type: SiteQuality
SIO_000300: 1.729288e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.9e-3

ClippingRankSum
type: SiteQuality
SIO_000300: 8.3e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -3.742e0

QD
type: SiteQuality
SIO_000300: 6.23e0

GenotypeQuality
all individuals: 1955
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2392
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 626
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 4056
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GenotypeQuality
all individuals: 2004
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variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7710
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6514
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 9.79431929480901e-5
allele num: 10210
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8552
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 790
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11206
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 58736
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.911e1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.67e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: -8.87e-1

QD
type: SiteQuality
SIO_000300: 9.48e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.12e0

VQSLOD
type: SiteQuality
SIO_000300: -3.96e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.16e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 1.324934e6

GenotypeQuality
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bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 6583
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 1981
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 827
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GenotypeQuality
all individuals: 2303
bin: 7.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6520
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7784
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.159554730983302e-4
allele num: 8624
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10330
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 794
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 59152
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11240
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 6.73e-1

QD
type: SiteQuality
SIO_000300: 1.385e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.71e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.27e-1

DP
type: SiteQuality
SIO_000300: 1.368226e6

MQRankSum
type: SiteQuality
SIO_000300: 2.96e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 4.76e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.0e-4

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1514
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GenotypeQuality
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bin: 9.75e1
variant carriers: 103

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 2318
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variant carriers: 0

GenotypeQuality
all individuals: 336
bin: 5.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 2
allele frequency: 3.064664419246092e-4
allele num: 6526
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.155535012710885e-4
allele num: 8654
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10396
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7816
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11254
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 794
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 98
allele frequency: 1.651499831479609e-3
allele num: 59340
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 6.01e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.2e-3

MQRankSum
type: SiteQuality
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QD
type: SiteQuality
SIO_000300: 1.347e1

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 8.699999999999999e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.18e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.031e0

DP
type: SiteQuality
SIO_000300: 1.39075e6

GenotypeQuality
all individuals: 839
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 350
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GenotypeQuality
all individuals: 3953
bin: 9.75e1
variant carriers: 1

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8794
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10672
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8034
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11322
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 808
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.659640853719255e-5
allele num: 60254
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6542
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.95e1

MQRankSum
type: SiteQuality
SIO_000300: -9.6e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.358e1

VQSLOD
type: SiteQuality
SIO_000300: 5.17e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.36e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.99e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.0e-4

DP
type: SiteQuality
SIO_000300: 1.452362e6

ClippingRankSum
type: SiteQuality
SIO_000300: -1.295e0

GenotypeQuality
all individuals: 1030
bin: 3.75e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 2441
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 2112
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GenotypeQuality
all individuals: 646
bin: 8.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8876
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 808
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6546
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8122
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 60652
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.807468733485996e-5
allele num: 11354
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 9.19793966151582e-5
allele num: 10872
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 1.1e0

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.6e-3

ClippingRankSum
type: SiteQuality
SIO_000300: -1.444e0

BaseQRankSum
type: SiteQuality
SIO_000300: 2.94e0

MQRankSum
type: SiteQuality
SIO_000300: 4.43e-1

MQ
type: SiteQuality
SIO_000300: 5.949e1

DP
type: SiteQuality
SIO_000300: 1.466624e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.35e0

QD
type: SiteQuality
SIO_000300: 1.594e1

GenotypeQuality
all individuals: 646
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 163
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1576
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 851
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 138
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1284
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 265
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 161
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 30998
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2452
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 6321
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3960
bin: 9.75e1
variant carriers: 1

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 61030
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10986
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.795074758135444e-5
allele num: 11370
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 808
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8916
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6554
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8190
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -2.818e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.1e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 3.17e-1

QD
type: SiteQuality
SIO_000300: 5.98e0

MQRankSum
type: SiteQuality
SIO_000300: -1.692e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

MQ
type: SiteQuality
SIO_000300: 5.837e1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.113e0

DP
type: SiteQuality
SIO_000300: 1.480266e6

GenotypeQuality
all individuals: 56
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 147
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 64
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 658
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 741
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3970
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 181
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 6347
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 34233
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2214
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 129
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1622
bin: 8.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11432
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11862
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9222
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6582
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 826
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.181753722524226e-4
allele num: 8462
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 62538
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -6.6e-1

MQRankSum
type: SiteQuality
SIO_000300: -8.100000000000001e-1

DP
type: SiteQuality
SIO_000300: 1.524574e6

BaseQRankSum
type: SiteQuality
SIO_000300: -3.9e-1

VQSLOD
type: SiteQuality
SIO_000300: 3.19e0

MQ
type: SiteQuality
SIO_000300: 6.041e1

FS
type: SiteQuality
SIO_000300: 1.758e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.6e-3

ClippingRankSum
type: SiteQuality
SIO_000300: -1.07e0

QD
type: SiteQuality
SIO_000300: 1.16e1

GenotypeQuality
all individuals: 877
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 111
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 113
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 55
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 35615
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 299
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 4194
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3975
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 104
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1635
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 6459
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 54
bin: 1.75e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9354
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.169043722235212e-4
allele num: 8554
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6596
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 12490
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 63264
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11474
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 2.014e1

FS
type: SiteQuality
SIO_000300: 4.26e0

VQSLOD
type: SiteQuality
SIO_000300: -2.533e0

DP
type: SiteQuality
SIO_000300: 1.542808e6

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: -2.082e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -6.81e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.3e-3

BaseQRankSum
type: SiteQuality
SIO_000300: 3.21e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.11e0

GenotypeQuality
all individuals: 1642
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 24
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 6566
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 36690
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3498
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 97
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 45
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 103
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 49
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 82
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 409
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2550
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 113
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 880
bin: 9.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11500
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8598
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 13044
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9476
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.129498654315578e-5
allele num: 63908
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 846
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6604
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 4.95e0

VQSLOD
type: SiteQuality
SIO_000300: 4.13e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.53e0

ClippingRankSum
type: SiteQuality
SIO_000300: -9.49e-1

DP
type: SiteQuality
SIO_000300: 1.558749e6

QD
type: SiteQuality
SIO_000300: 1.588e1

MQRankSum
type: SiteQuality
SIO_000300: -6.63e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.6e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.0e-3

MQ
type: SiteQuality
SIO_000300: 5.987e1

GenotypeQuality
all individuals: 50
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 62
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2348
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 77
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 675
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 73
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2618
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 6945
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 92
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1677
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 40256
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 887
bin: 9.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8646
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.020199959192002e-4
allele num: 9802
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11558
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 888
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16126
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66138
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.879e1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.2e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.739e0

MQRankSum
type: SiteQuality
SIO_000300: -1.01e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.6e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.77e-1

DP
type: SiteQuality
SIO_000300: 1.617309e6

QD
type: SiteQuality
SIO_000300: 1.097e1

FS
type: SiteQuality
SIO_000300: 1.177e0

VQSLOD
type: SiteQuality
SIO_000300: -2.358e-1

GenotypeQuality
all individuals: 464
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1656
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 673
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4182
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 2350
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 7
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 40423
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 41
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 58
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 47
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 874
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 46
bin: 5.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11560
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9830
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.507886245061673e-5
allele num: 66318
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16312
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.612e1

DP
type: SiteQuality
SIO_000300: 1.640616e6

FS
type: SiteQuality
SIO_000300: 6.26e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.13e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -4.04e-1

VQSLOD
type: SiteQuality
SIO_000300: 3.27e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.94e-2

BaseQRankSum
type: SiteQuality
SIO_000300: 4.97e0

MQRankSum
type: SiteQuality
SIO_000300: 2.53e-1

MQ
type: SiteQuality
SIO_000300: 5.964e1

GenotypeQuality
all individuals: 41
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 673
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 39
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 40423
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 58
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 156
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 67
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 874
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 6968
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2350
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 4.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 57
allele frequency: 8.594951596851534e-4
allele num: 66318
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 187
allele frequency: 2.827335954036891e-2
allele num: 6614
num of homozygotes: 5

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16312
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11560
num of homozygotes: 0

Other
type: Population
allele count: 6
allele frequency: 6.711409395973154e-3
allele num: 894
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9830
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 4.97e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.13e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.53e-1

VQSLOD
type: SiteQuality
SIO_000300: 3.27e0

FS
type: SiteQuality
SIO_000300: 6.26e-1

QD
type: SiteQuality
SIO_000300: 1.612e1

ClippingRankSum
type: SiteQuality
SIO_000300: -4.04e-1

DP
type: SiteQuality
SIO_000300: 1.640616e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.94e-2

MQ
type: SiteQuality
SIO_000300: 5.964e1

GenotypeQuality
all individuals: 40
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 40616
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 135
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 685
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 8
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 10
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 49
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 896
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4014
bin: 9.75e1
variant carriers: 25

GenotypeQuality
all individuals: 2618
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 29
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7022
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1673
bin: 8.25e1
variant carriers: 0

South Asian
type: Population
allele count: 24
allele frequency: 1.465559355153884e-3
allele num: 16376
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9860
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11564
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8646
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.505797319680771e-5
allele num: 66410
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 900
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 3.33e0

MQ
type: SiteQuality
SIO_000300: 5.936e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.0e-4

MQRankSum
type: SiteQuality
SIO_000300: -9.0e-2

QD
type: SiteQuality
SIO_000300: 1.286e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.26e-1

DP
type: SiteQuality
SIO_000300: 1.626359e6

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -4.205e0

ClippingRankSum
type: SiteQuality
SIO_000300: -5.41e-1

GenotypeQuality
all individuals: 36
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 27
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 36
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 316
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 105
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 3
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 7052
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 35
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 40736
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 896
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2369
bin: 7.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16452
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66508
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11564
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.012145748987854e-4
allele num: 9880
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 900
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8646
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.221e0

VQSLOD
type: SiteQuality
SIO_000300: 2.37e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.32e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.0e-4

MQRankSum
type: SiteQuality
SIO_000300: 1.26e0

FS
type: SiteQuality
SIO_000300: 3.701e0

DP
type: SiteQuality
SIO_000300: 1.62845e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.03e0

BaseQRankSum
type: SiteQuality
SIO_000300: 6.04e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 9.75e1
variant carriers: 1

GenotypeQuality
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bin: 7.75e1
variant carriers: 0

GenotypeQuality
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bin: 7.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11566
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 902
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16472
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66534
num of homozygotes: 0

African
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allele count: 1
allele frequency: 1.010713563776026e-4
allele num: 9894
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.24e0

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.786e0

MQRankSum
type: SiteQuality
SIO_000300: 1.0e-3

QD
type: SiteQuality
SIO_000300: 1.299e1

ClippingRankSum
type: SiteQuality
SIO_000300: -5.72e-1

MQ
type: SiteQuality
SIO_000300: 5.961e1

VQSLOD
type: SiteQuality
SIO_000300: 1.36e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

DP
type: SiteQuality
SIO_000300: 1.629516e6

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 4.25e1
variant carriers: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 902
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11566
num of homozygotes: 0

African
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allele count: 1
allele frequency: 1.010305112143867e-4
allele num: 9898
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66530
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16472
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.629722e6

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.97e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.0e-4

VQSLOD
type: SiteQuality
SIO_000300: -2.74e0

MQ
type: SiteQuality
SIO_000300: 5.859e1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.72e-1

MQRankSum
type: SiteQuality
SIO_000300: 8.100000000000001e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.811e0

QD
type: SiteQuality
SIO_000300: 6.81e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 3

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

Latino
type: Population
allele count: 3
allele frequency: 2.593809441466367e-4
allele num: 11566
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 902
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 9902
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66548
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16486
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.94e-1

VQSLOD
type: SiteQuality
SIO_000300: 5.51e-1

MQ
type: SiteQuality
SIO_000300: 5.958e1

QD
type: SiteQuality
SIO_000300: 1.206e1

DP
type: SiteQuality
SIO_000300: 1.630385e6

MQRankSum
type: SiteQuality
SIO_000300: 1.12e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

FS
type: SiteQuality
SIO_000300: 7.713e0

BaseQRankSum
type: SiteQuality
SIO_000300: -4.319e0

ClippingRankSum
type: SiteQuality
SIO_000300: -3.9e-2

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66626
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9984
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.058403004967891e-5
allele num: 16506
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -6.42e-1

VQSLOD
type: SiteQuality
SIO_000300: 7.000000000000001e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -1.9e-2

QD
type: SiteQuality
SIO_000300: 1.664e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.68e-1

MQ
type: SiteQuality
SIO_000300: 5.939e1

BaseQRankSum
type: SiteQuality
SIO_000300: 9.28e-1

DP
type: SiteQuality
SIO_000300: 1.632526e6

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 7.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9986
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66630
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.058403004967891e-5
allele num: 16506
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.765e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.29e0

FS
type: SiteQuality
SIO_000300: 3.901e0

MQRankSum
type: SiteQuality
SIO_000300: 1.3e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

DP
type: SiteQuality
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VQSLOD
type: SiteQuality
SIO_000300: -2.629e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.8e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

QD
type: SiteQuality
SIO_000300: 1.457e1

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 6

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 21
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variant carriers: 0

GenotypeQuality
all individuals: 1679
bin: 8.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8646
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10064
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16508
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66666
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 6
allele frequency: 9.071666162685213e-4
allele num: 6614
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.63434e6

InbreedingCoeff
type: SiteQuality
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VQSLOD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
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FS
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.942e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.38e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.7e0

QD
type: SiteQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 3.25e1
variant carriers: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.15606936416185e-4
allele num: 8650
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16508
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10090
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66664
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.62e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
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FS
type: SiteQuality
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VQSLOD
type: SiteQuality
SIO_000300: 1.54e-1

QD
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 1.634248e6

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 6.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.056935190793458e-5
allele num: 16510
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.912767644726408e-5
allele num: 10088
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

European (Non-Finnish)
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allele count: 4
allele frequency: 6.000060000600006e-5
allele num: 66666
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 4.3e-2

BaseQRankSum
type: SiteQuality
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FS
type: SiteQuality
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QD
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.97e1

VQSLOD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 1.634599e6

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 12
bin: 4.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8646
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10098
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.499970000599988e-5
allele num: 66668
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 2.09e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

MQ
type: SiteQuality
SIO_000300: 5.883e1

DP
type: SiteQuality
SIO_000300: 1.634568e6

QD
type: SiteQuality
SIO_000300: 1.21e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.27e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.925e0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.54e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.42e-1

GenotypeQuality
all individuals: 17
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 41103
bin: 6.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 1

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

GenotypeQuality
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bin: 9.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 7071
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 4.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.49934029027228e-5
allele num: 66696
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10256
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

MQRankSum
type: SiteQuality
SIO_000300: 4.19e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.146e0

DP
type: SiteQuality
SIO_000300: 1.636333e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.15e0

VQSLOD
type: SiteQuality
SIO_000300: 5.47e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 3.105e0

QD
type: SiteQuality
SIO_000300: 1.357e1

ClippingRankSum
type: SiteQuality
SIO_000300: -2.22e0

GenotypeQuality
all individuals: 902
bin: 9.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 41076
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variant carriers: 0

GenotypeQuality
all individuals: 1678
bin: 8.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66700
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.737098344693281e-5
allele num: 10270
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 4.09e-1

FS
type: SiteQuality
SIO_000300: 1.617e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.27e0

DP
type: SiteQuality
SIO_000300: 1.636624e6

MQ
type: SiteQuality
SIO_000300: 5.915e1

MQRankSum
type: SiteQuality
SIO_000300: 7.46e-1

VQSLOD
type: SiteQuality
SIO_000300: 8.799999999999999e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -6.797e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

QD
type: SiteQuality
SIO_000300: 1.086e1

GenotypeQuality
all individuals: 0
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 2
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 1679
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variant carriers: 0

GenotypeQuality
all individuals: 902
bin: 9.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10308
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.643042350907519e-5
allele num: 11570
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66706
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 1.07e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.888e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.07e0

MQRankSum
type: SiteQuality
SIO_000300: 3.59e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 5.17e-1

FS
type: SiteQuality
SIO_000300: 5.066e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

MQ
type: SiteQuality
SIO_000300: 5.987e1

QD
type: SiteQuality
SIO_000300: 1.257e1

DP
type: SiteQuality
SIO_000300: 1.636956e6

GenotypeQuality
all individuals: 81
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 16
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 13
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 32
bin: 5.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10322
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.499115521842113e-5
allele num: 66706
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.637162e6

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

QD
type: SiteQuality
SIO_000300: 1.264e1

MQ
type: SiteQuality
SIO_000300: 5.977e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.379999999999999e-1

MQRankSum
type: SiteQuality
SIO_000300: -2.45e-1

FS
type: SiteQuality
SIO_000300: 4.045e0

VQSLOD
type: SiteQuality
SIO_000300: 1.01e0

BaseQRankSum
type: SiteQuality
SIO_000300: 2.61e0

ClippingRankSum
type: SiteQuality
SIO_000300: -6.61e-1

GenotypeQuality
all individuals: 14
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 901
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 2

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 12
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 41171
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variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 4.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10380
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66720
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Latino
type: Population
allele count: 2
allele frequency: 1.728309713100588e-4
allele num: 11572
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 9.83e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 6.25e0

MQRankSum
type: SiteQuality
SIO_000300: 1.14e0

QD
type: SiteQuality
SIO_000300: 1.521e1

MQ
type: SiteQuality
SIO_000300: 5.996e1

VQSLOD
type: SiteQuality
SIO_000300: 3.87e-1

FS
type: SiteQuality
SIO_000300: 4.239e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.4e-1

DP
type: SiteQuality
SIO_000300: 1.63807e6

GenotypeQuality
all individuals: 900
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 9.75e1
variant carriers: 75

GenotypeQuality
all individuals: 687
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variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 4.25e1
variant carriers: 0

East Asian
type: Population
allele count: 63
allele frequency: 7.279870580078576e-3
allele num: 8654
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66724
num of homozygotes: 0

African
type: Population
allele count: 4
allele frequency: 3.853564547206166e-4
allele num: 10380
num of homozygotes: 0

South Asian
type: Population
allele count: 7
allele frequency: 4.239854633555421e-4
allele num: 16510
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.641548565502938e-5
allele num: 11572
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 3.44e0

FS
type: SiteQuality
SIO_000300: 5.22e-1

MQ
type: SiteQuality
SIO_000300: 5.969e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.42e-1

DP
type: SiteQuality
SIO_000300: 1.643454e6

MQRankSum
type: SiteQuality
SIO_000300: -2.7e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -4.984e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.0e-4

QD
type: SiteQuality
SIO_000300: 1.225e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.09e-1

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

GenotypeQuality
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bin: 5.25e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 4.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 18
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GenotypeQuality
all individuals: 4007
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variant carriers: 1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 1681
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 7087
bin: 6.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11572
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66722
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.633911368015414e-5
allele num: 10380
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 7.45e-1

FS
type: SiteQuality
SIO_000300: 3.269e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

QD
type: SiteQuality
SIO_000300: 2.046e1

MQ
type: SiteQuality
SIO_000300: 5.884e1

VQSLOD
type: SiteQuality
SIO_000300: 1.17e0

DP
type: SiteQuality
SIO_000300: 1.638784e6

ClippingRankSum
type: SiteQuality
SIO_000300: 4.45e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.011e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.389e0

GenotypeQuality
all individuals: 36
bin: 2.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 28
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variant carriers: 0

GenotypeQuality
all individuals: 8
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 25
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GenotypeQuality
all individuals: 13
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 2378
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 4.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11572
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.498845888665727e-5
allele num: 66718
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.056935190793458e-5
allele num: 16510
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10386
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

FS
type: SiteQuality
SIO_000300: 6.402e0

MQRankSum
type: SiteQuality
SIO_000300: 5.77e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -5.486e0

DP
type: SiteQuality
SIO_000300: 1.639345e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.81e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.41e0

MQ
type: SiteQuality
SIO_000300: 5.964e1

QD
type: SiteQuality
SIO_000300: 1.466e1

VQSLOD
type: SiteQuality
SIO_000300: 5.600000000000001e-1

GenotypeQuality
all individuals: 2
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 30
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 4010
bin: 9.75e1
variant carriers: 3

GenotypeQuality
all individuals: 41194
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21
bin: 4.75e1
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GenotypeQuality
all individuals: 2627
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 688
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 903
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7094
bin: 6.75e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.496133325340207e-5
allele num: 66724
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11574
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10392
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 3.49e0

MQ
type: SiteQuality
SIO_000300: 5.957e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

DP
type: SiteQuality
SIO_000300: 1.639358e6

FS
type: SiteQuality
SIO_000300: 8.52e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.19e0

ClippingRankSum
type: SiteQuality
SIO_000300: -7.6e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: -6.7e-2

VQSLOD
type: SiteQuality
SIO_000300: 5.7e-1

QD
type: SiteQuality
SIO_000300: 1.426e1

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

GenotypeQuality
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bin: 5.25e1
variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 7

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 3.75e1
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GenotypeQuality
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bin: 2.5e0
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GenotypeQuality
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bin: 6.75e1
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GenotypeQuality
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GenotypeQuality
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bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 7
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7
bin: 4.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10398
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 7
allele frequency: 1.049003446725611e-4
allele num: 66730
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.63984e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.909999999999999e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.01e0

ClippingRankSum
type: SiteQuality
SIO_000300: -6.12e-1

MQ
type: SiteQuality
SIO_000300: 5.952e1

MQRankSum
type: SiteQuality
SIO_000300: -4.95e-1

FS
type: SiteQuality
SIO_000300: 1.745e0

BaseQRankSum
type: SiteQuality
SIO_000300: 3.48e0

QD
type: SiteQuality
SIO_000300: 1.34e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

GenotypeQuality
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bin: 6.75e1
variant carriers: 0

GenotypeQuality
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bin: 2.5e0
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
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bin: 3.75e1
variant carriers: 0

GenotypeQuality
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bin: 4.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66728
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.617234083477592e-5
allele num: 10398
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.0e-1

QD
type: SiteQuality
SIO_000300: 1.248e1

DP
type: SiteQuality
SIO_000300: 1.63953e6

FS
type: SiteQuality
SIO_000300: 2.548e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 7.1e-1

MQ
type: SiteQuality
SIO_000300: 5.851e1

MQRankSum
type: SiteQuality
SIO_000300: -1.52e-1

VQSLOD
type: SiteQuality
SIO_000300: -2.933e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -4.0e-2

GenotypeQuality
all individuals: 8
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 11
bin: 5.75e1
variant carriers: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.056935190793458e-5
allele num: 16510
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10400
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66734
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 7.11e-1

MQ
type: SiteQuality
SIO_000300: 5.962e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

QD
type: SiteQuality
SIO_000300: 1.198e1

DP
type: SiteQuality
SIO_000300: 1.63975e6

VQSLOD
type: SiteQuality
SIO_000300: 1.99e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.599e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.5e-2

MQRankSum
type: SiteQuality
SIO_000300: -1.271e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.97e-1

GenotypeQuality
all individuals: 8
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 6

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 3
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variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 7.5e0
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

Latino
type: Population
allele count: 4
allele frequency: 3.455425017277125e-4
allele num: 11576
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 2.996703626011388e-5
allele num: 66740
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

FS
type: SiteQuality
SIO_000300: 5.23e-1

MQ
type: SiteQuality
SIO_000300: 5.973e1

MQRankSum
type: SiteQuality
SIO_000300: 1.29e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.02e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.78e0

QD
type: SiteQuality
SIO_000300: 1.193e1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.4e-2

DP
type: SiteQuality
SIO_000300: 1.640452e6

ClippingRankSum
type: SiteQuality
SIO_000300: 2.0e-2

GenotypeQuality
all individuals: 0
bin: 2.5e0
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 7097
bin: 6.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 1.511944360447536e-4
allele num: 6614
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66740
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 2.22e0

BaseQRankSum
type: SiteQuality
SIO_000300: -4.127e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: -1.376e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.612e0

QD
type: SiteQuality
SIO_000300: 1.277e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.0e-4

DP
type: SiteQuality
SIO_000300: 1.640124e6

FS
type: SiteQuality
SIO_000300: 1.2614e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.36e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 8.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66740
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.155535012710885e-4
allele num: 8654
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.649521e6

VQSLOD
type: SiteQuality
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MQRankSum
type: SiteQuality
SIO_000300: 1.47e-1

MQ
type: SiteQuality
SIO_000300: 5.973e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.12e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.13e-2

FS
type: SiteQuality
SIO_000300: 5.18e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.84e0

QD
type: SiteQuality
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ClippingRankSum
type: SiteQuality
SIO_000300: -2.93e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 9.75e1
variant carriers: 97

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

African
type: Population
allele count: 93
allele frequency: 8.938869665513265e-3
allele num: 10404
num of homozygotes: 1

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.498351813005694e-5
allele num: 66740
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

Latino
type: Population
allele count: 3
allele frequency: 2.591568762957844e-4
allele num: 11576
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.056935190793458e-5
allele num: 16510
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.649521e6

MQRankSum
type: SiteQuality
SIO_000300: 1.47e-1

MQ
type: SiteQuality
SIO_000300: 5.973e1

QD
type: SiteQuality
SIO_000300: 1.445e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.12e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.84e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.13e-2

ClippingRankSum
type: SiteQuality
SIO_000300: -2.93e-1

FS
type: SiteQuality
SIO_000300: 5.18e-1

VQSLOD
type: SiteQuality
SIO_000300: 4.82e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 6.25e1
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GenotypeQuality
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variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.498351813005694e-5
allele num: 66740
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

African
type: Population
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num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -8.949e-1

MQ
type: SiteQuality
SIO_000300: 5.871e1

FS
type: SiteQuality
SIO_000300: 6.71e-1

MQRankSum
type: SiteQuality
SIO_000300: 4.61e-1

QD
type: SiteQuality
SIO_000300: 1.235e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: -7.63e-1

BaseQRankSum
type: SiteQuality
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DP
type: SiteQuality
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ClippingRankSum
type: SiteQuality
SIO_000300: 1.28e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 7.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Latino
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allele count: 1
allele frequency: 8.638562543192812e-5
allele num: 11576
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East Asian
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allele frequency: 0.0e0
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num of homozygotes: 0

South Asian
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66740
num of homozygotes: 0

Other
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allele frequency: 0.0e0
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BaseQRankSum
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MQRankSum
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SIO_000300: 1.44e-1

VQSLOD
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InbreedingCoeff
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FS
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SIO_000300: 4.334e0

QD
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ReadPosRankSum
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SIO_000300: 1.72e-1

ClippingRankSum
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SIO_000300: -2.4e-1

MQ
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DP
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

African
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allele frequency: 1.922337562475971e-4
allele num: 10404
num of homozygotes: 0

Other
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allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
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South Asian
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allele frequency: 0.0e0
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Latino
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allele frequency: 0.0e0
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num of homozygotes: 0

European (Finnish)
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allele frequency: 0.0e0
allele num: 6614
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East Asian
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allele frequency: 0.0e0
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MQRankSum
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QD
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ClippingRankSum
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ReadPosRankSum
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FS
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MQ
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InbreedingCoeff
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BaseQRankSum
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VQSLOD
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DP
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

European (Non-Finnish)
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allele frequency: 1.4983967155144e-5
allele num: 66738
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

South Asian
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allele frequency: 0.0e0
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num of homozygotes: 0

Latino
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Other
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East Asian
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ReadPosRankSum
type: SiteQuality
SIO_000300: -2.34e-1

MQ
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SIO_000300: 5.891e1

MQRankSum
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FS
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SIO_000300: 1.621e0

QD
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InbreedingCoeff
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SIO_000300: 5.0e-4

VQSLOD
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ClippingRankSum
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SIO_000300: 1.88e-1

DP
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BaseQRankSum
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SIO_000300: -1.309e0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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Latino
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allele frequency: 0.0e0
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num of homozygotes: 0

European (Finnish)
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele count: 2
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allele num: 66738
num of homozygotes: 0

Other
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East Asian
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African
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South Asian
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MQ
type: SiteQuality
SIO_000300: 6.069e1

DP
type: SiteQuality
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InbreedingCoeff
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SIO_000300: 4.0e-4

QD
type: SiteQuality
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ClippingRankSum
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SIO_000300: 1.18e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
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SIO_000300: 1.03e0

VQSLOD
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ReadPosRankSum
type: SiteQuality
SIO_000300: 8.400000000000001e-2

BaseQRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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South Asian
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allele num: 16510
num of homozygotes: 0

Latino
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European (Finnish)
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allele frequency: 0.0e0
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num of homozygotes: 0

African
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele frequency: 0.0e0
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East Asian
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Other
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ClippingRankSum
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ReadPosRankSum
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FS
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QD
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MQ
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MQRankSum
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VQSLOD
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InbreedingCoeff
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DP
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BaseQRankSum
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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East Asian
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num of homozygotes: 0

Other
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Latino
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allele num: 11576
num of homozygotes: 0

European (Finnish)
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African
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South Asian
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European (Non-Finnish)
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BaseQRankSum
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MQRankSum
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MQ
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ClippingRankSum
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DP
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VQSLOD
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FS
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QD
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InbreedingCoeff
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ReadPosRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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European (Non-Finnish)
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num of homozygotes: 0

African
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East Asian
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Latino
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South Asian
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Other
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European (Finnish)
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FS
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InbreedingCoeff
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BaseQRankSum
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ReadPosRankSum
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MQ
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MQRankSum
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ClippingRankSum
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VQSLOD
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DP
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QD
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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South Asian
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Latino
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European (Non-Finnish)
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African
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European (Finnish)
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Other
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East Asian
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ClippingRankSum
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FS
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DP
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InbreedingCoeff
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ReadPosRankSum
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MQ
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MQRankSum
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QD
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VQSLOD
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BaseQRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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African
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Latino
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European (Finnish)
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European (Non-Finnish)
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East Asian
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South Asian
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MQRankSum
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BaseQRankSum
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MQ
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QD
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DP
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VQSLOD
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InbreedingCoeff
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FS
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ReadPosRankSum
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ClippingRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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European (Finnish)
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Other
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East Asian
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allele frequency: 0.0e0
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Latino
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European (Non-Finnish)
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African
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South Asian
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InbreedingCoeff
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ClippingRankSum
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MQ
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ReadPosRankSum
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VQSLOD
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FS
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MQRankSum
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BaseQRankSum
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QD
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DP
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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East Asian
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Other
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African
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele frequency: 2.547427098630383e-4
allele num: 66734
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Latino
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allele num: 11578
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South Asian
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European (Finnish)
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allele frequency: 0.0e0
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DP
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FS
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BaseQRankSum
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ReadPosRankSum
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MQRankSum
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InbreedingCoeff
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QD
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VQSLOD
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MQ
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ClippingRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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Other
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European (Finnish)
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African
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allele frequency: 0.0e0
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European (Non-Finnish)
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East Asian
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South Asian
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allele frequency: 8.843125378558449e-3
allele num: 16510
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Latino
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BaseQRankSum
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ReadPosRankSum
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ClippingRankSum
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VQSLOD
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MQ
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MQRankSum
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InbreedingCoeff
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FS
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DP
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QD
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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Other
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African
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allele frequency: 0.0e0
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European (Finnish)
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allele frequency: 0.0e0
allele num: 6614
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South Asian
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East Asian
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Latino
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele frequency: 1.498441620714457e-5
allele num: 66736
num of homozygotes: 0

VQSLOD
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MQRankSum
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InbreedingCoeff
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ReadPosRankSum
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QD
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FS
type: SiteQuality
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BaseQRankSum
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ClippingRankSum
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MQ
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DP
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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East Asian
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Other
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African
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allele frequency: 0.0e0
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European (Finnish)
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allele frequency: 0.0e0
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South Asian
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European (Non-Finnish)
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allele frequency: 1.498441620714457e-5
allele num: 66736
num of homozygotes: 0

Latino
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BaseQRankSum
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DP
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FS
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MQRankSum
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QD
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ReadPosRankSum
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MQ
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VQSLOD
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ClippingRankSum
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InbreedingCoeff
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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Other
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African
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European (Finnish)
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European (Non-Finnish)
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Latino
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South Asian
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East Asian
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DP
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MQRankSum
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MQ
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ReadPosRankSum
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QD
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ClippingRankSum
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InbreedingCoeff
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FS
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VQSLOD
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BaseQRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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Latino
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South Asian
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East Asian
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African
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European (Non-Finnish)
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European (Finnish)
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BaseQRankSum
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InbreedingCoeff
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ClippingRankSum
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VQSLOD
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DP
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MQRankSum
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ReadPosRankSum
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QD
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FS
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MQ
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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East Asian
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Other
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South Asian
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African
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Latino
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European (Finnish)
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European (Non-Finnish)
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InbreedingCoeff
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MQRankSum
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BaseQRankSum
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MQ
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FS
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ReadPosRankSum
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DP
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VQSLOD
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QD
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GenotypeQuality
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East Asian
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Latino
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Other
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South Asian
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European (Finnish)
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African
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European (Non-Finnish)
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VQSLOD
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ClippingRankSum
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MQRankSum
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QD
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BaseQRankSum
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MQ
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FS
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InbreedingCoeff
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ReadPosRankSum
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DP
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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all individuals: 7
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2373
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 5
bin: 2.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.155535012710885e-4
allele num: 8654
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11578
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66738
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 6.71e-1

DP
type: SiteQuality
SIO_000300: 1.642536e6

MQ
type: SiteQuality
SIO_000300: 5.97e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

QD
type: SiteQuality
SIO_000300: 9.65e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.77e-1

MQRankSum
type: SiteQuality
SIO_000300: -7.57e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.5e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.0e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.9e-1