rs1613662

Homo sapiens
G>A
GP6 : Missense Variant
LOC107985325 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0156 (4684/29938,GnomAD)
G==0186 (5436/29118,TOPMED)
G==0186 (4181/22466,ExAC)
A=0175 (2075/11860,GO-ESP)
G==0157 (788/5008,1000G)
G==0164 (631/3854,ALSPAC)
G==0163 (603/3708,TWINSUK)
chr19:55025227 (GRCh38.p7) (19q13.42)
CD
GWASdb2
24   publication(s)
See rs on genome
108 Enhancers around
28 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 19NC_000019.10:g.55025227G>A
GRCh37.p13 chr 19 fix patch HG1079_PATCHNW_004166865.1:g.999595G>A
GP6 RefSeqGene LRG_560
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF2_CTG3_1NW_003571061.2:g.737388G>A
GRCh37.p13 chr 19 novel patch HSCHR19LRC_PGF2_CTG1NW_003571061.1:g.737387G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_T_CTG3_1NW_003571059.2:g.943592G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_S_CTG3_1NW_003571058.2:g.1007299G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_J_CTG3_1NW_003571057.2:g.1032750G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_I_CTG3_1NW_003571056.2:g.1005213G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX2_CTG3_1NW_003571055.2:g.670429G>A
GRCh37.p13 chr 19 novel patch HSCHR19LRC_COX2_CTG1NW_003571055.1:g.670428G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1NW_003571060.1:g.928009G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1NW_003571054.1:g.928625G>A
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1NT_187693.1:g.1007709G>A
GRCh37.p13 chr 19NC_000019.9:g.55536595G>A

Gene: GP6, glycoprotein VI platelet(minus strand)

Molecule type Change Amino acid[Codon] SO Term
GP6 transcript variant 3NM_001256017.2:c.N/AIntron Variant
GP6 transcript variant 1NM_001083899.2:c....NM_001083899.2:c.655C>TP [CCG]> S [TCG]Coding Sequence Variant
platelet glycoprotein VI isoform 1 precursorNP_001077368.2:p....NP_001077368.2:p.Pro219SerP [Pro]> S [Ser]Missense Variant
GP6 transcript variant 2NM_016363.5:c.655C>TP [CCG]> S [TCG]Coding Sequence Variant
platelet glycoprotein VI isoform 2 precursorNP_057447.5:p.Pro...NP_057447.5:p.Pro219SerP [Pro]> S [Ser]Missense Variant

Gene: LOC107985325, uncharacterized LOC107985325(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107985325 transcript variant X1XR_001754012.1:n.N/AIntron Variant
LOC107985325 transcript variant X2XR_001754013.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.253A=0.747
1000GenomesAmericanSub694G=0.090A=0.910
1000GenomesEast AsianSub1008G=0.034A=0.966
1000GenomesEuropeSub1006G=0.145A=0.855
1000GenomesGlobalStudy-wide5008G=0.157A=0.843
1000GenomesSouth AsianSub978G=0.220A=0.780
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.164A=0.836
The Exome Aggregation ConsortiumAmericanSub2980G=0.220A=0.780
The Exome Aggregation ConsortiumAsianSub8678G=0.198A=0.802
The Exome Aggregation ConsortiumEuropeSub10612G=0.168A=0.832
The Exome Aggregation ConsortiumGlobalStudy-wide22466G=0.186A=0.813
The Exome Aggregation ConsortiumOtherSub196G=0.130A=0.870
The Genome Aggregation DatabaseAfricanSub8702G=0.222A=0.778
The Genome Aggregation DatabaseAmericanSub838G=0.090A=0.910
The Genome Aggregation DatabaseEast AsianSub1616G=0.017A=0.983
The Genome Aggregation DatabaseEuropeSub18480G=0.139A=0.860
The Genome Aggregation DatabaseGlobalStudy-wide29938G=0.156A=0.843
The Genome Aggregation DatabaseOtherSub302G=0.250A=0.750
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.186A=0.813
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.163A=0.837
PMID Title Author Journal
22821001Variability of GP6 gene in patients with sticky platelet syndrome and deep venous thrombosis and/or pulmonary embolism.Kotulicova DBlood Coagul Fibrinolysis
18349091Gene variants associated with deep vein thrombosis.Bezemer IDJAMA
24456740Apolipoprotein E polymorphism is associated with lower extremity deep venous thrombosis: color-flow Doppler ultrasound evaluation.Zhu SLipids Health Dis
25091233Association of F11 polymorphism rs2289252 with deep vein thrombosis and related phenotypes in population of Latvia.Rovite VThromb Res
23958962Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.Gelernter JMol Psychiatry
23124848Brief Report: Single-nucleotide polymorphisms in VKORC1 are risk factors for systemic lupus erythematosus in Asians.Kaiser RArthritis Rheum
27143073[Pharmacogenomics study of 620 whole-exome sequencing: focusing on aspirin application].Yang LZhonghua Er Ke Za Zhi
20610812The genetics of normal platelet reactivity.Kunicki TJBlood
20031567An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of venous thromboembolism: The Women's Genome Health Study.Zee RYCirc Cardiovasc Genet
25901734Effect of platelet receptor gene polymorphisms on outcomes in ST-elevation myocardial infarction patients after percutaneous coronary intervention.Zhang JHPlatelets
19786296Platelet glycoprotein GP VI 13254C allele is an independent risk factor of premature myocardial infarction.Motovska ZThromb Res
23150947Single nucleotide polymorphisms and the risk of venous thrombosis: results from a Danish case-cohort study.El-Galaly TCBr J Haematol
19278955Common susceptibility alleles are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach.Tregouet DABlood
20227257Polymorphisms in the platelet-specific collagen receptor GP6 are associated with risk of nonfatal myocardial infarction in Caucasians.Shaffer JRNutr Metab Cardiovasc Dis
25741868Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.Richards SGenet Med
25093390Genetic polymorphisms of platelet receptors in patients with acute myocardial infarction and resistance to antiplatelet therapy.Ulehlova JGenet Test Mol Biomarkers
25360888Genetic determinants of on-aspirin platelet reactivity: focus on the influence of PEAR1.Wurtz MPLoS One
21084706Genetic regulation of platelet receptor expression and function: application in clinical practice and drug development.Williams MSArterioscler Thromb Vasc Biol
21854539Genetic determinants of platelet reactivity during acetylsalicylic acid therapy in diabetic patients: evaluation of 27 polymorphisms within candidate genes.Postula MJ Thromb Haemost
22133274Polymorphisms of PAI-1 and platelet GP Ia may associate with impairment of renal function and thrombocytopenia in Puumala hantavirus infection.Laine OThromb Res
21232005New gene variants associated with venous thrombosis: a replication study in White and Black Americans.Austin HJ Thromb Haemost
20526338Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists.Johnson ADNat Genet
22901851Platelet aggregation abnormalities in patients with fetal losses: the GP6 gene polymorphism.Sokol JFertil Steril
27766050Causes of venous thrombosis.Rosendaal FRThromb J

P-Value

SNP ID p-value Traits Study
rs16136620.000574cocaine dependence23958962

eQTL of rs1613662 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr19:55536595GP6ENSG00000088053.7G>A9.0091e-6-13037Cerebellum
Chr19:55536595GP6ENSG00000088053.7G>A1.2367e-4-13037Cerebellar_Hemisphere

meQTL of rs1613662 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr19950706950795E067-48800
chr19983359983479E067-16116
chr19983553983756E067-15839
chr1910156081015844E06716013
chr1910158511016391E06716256
chr1910164891017758E06716894
chr1910177871017841E06718192
chr1910178421017926E06718247
chr1910180581018350E06718463
chr1910184261018691E06718831
chr1910187601018893E06719165
chr19983359983479E068-16116
chr19983553983756E068-15839
chr1910156081015844E06816013
chr1910158511016391E06816256
chr1910164891017758E06816894
chr1910177871017841E06818192
chr1910178421017926E06818247
chr1910180581018350E06818463
chr1910184261018691E06818831
chr1910187601018893E06819165
chr19983359983479E069-16116
chr19983553983756E069-15839
chr19995473995566E069-4029
chr1910158511016391E06916256
chr1910164891017758E06916894
chr1910177871017841E06918192
chr1910178421017926E06918247
chr1910180581018350E06918463
chr1910184261018691E06918831
chr1910187601018893E06919165
chr19955812957516E070-42079
chr19983359983479E070-16116
chr19983553983756E070-15839
chr19985442985779E070-13816
chr19985854986068E070-13527
chr1910156081015844E07016013
chr1910158511016391E07016256
chr1910164891017758E07016894
chr1910177871017841E07018192
chr1910178421017926E07018247
chr1910180581018350E07018463
chr1910184261018691E07018831
chr1910187601018893E07019165
chr1910427041042894E07043109
chr1910428971043079E07043302
chr19983359983479E071-16116
chr19983553983756E071-15839
chr1910156081015844E07116013
chr1910158511016391E07116256
chr1910164891017758E07116894
chr1910177871017841E07118192
chr1910178421017926E07118247
chr1910180581018350E07118463
chr1910184261018691E07118831
chr1910187601018893E07119165
chr19983359983479E072-16116
chr19983553983756E072-15839
chr1910158511016391E07216256
chr1910164891017758E07216894
chr1910177871017841E07218192
chr1910178421017926E07218247
chr1910180581018350E07218463
chr1910184261018691E07218831
chr1910187601018893E07219165
chr1910156081015844E07316013
chr1910158511016391E07316256
chr1910164891017758E07316894
chr1910177871017841E07318192
chr1910178421017926E07318247
chr1910180581018350E07318463
chr1910184261018691E07318831
chr1910187601018893E07319165
chr1910415611042684E07341966
chr19983359983479E074-16116
chr19983553983756E074-15839
chr1910158511016391E07416256
chr1910164891017758E07416894
chr1910177871017841E07418192
chr1910178421017926E07418247
chr1910180581018350E07418463
chr1910184261018691E07418831
chr1910187601018893E07419165
chr19983359983479E081-16116
chr19983553983756E081-15839
chr19985276985326E081-14269
chr19985442985779E081-13816
chr1910164891017758E08116894
chr1910177871017841E08118192
chr1910178421017926E08118247
chr1910180581018350E08118463
chr1910184261018691E08118831
chr1910187601018893E08119165
chr1910415611042684E08141966
chr1910427041042894E08143109
chr1910428971043079E08143302
chr19985276985326E082-14269
chr19985442985779E082-13816
chr19985854986068E082-13527
chr19986132986303E082-13292
chr19986710986821E082-12774
chr1910158511016391E08216256
chr1910164891017758E08216894
chr1910177871017841E08218192
chr1910178421017926E08218247
chr1910180581018350E08218463
chr1910184261018691E08218831
chr1910187601018893E08219165










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr19983831985184E067-14411
chr1910195561022221E06719961
chr1910259091029005E06726314
chr19983831985184E068-14411
chr1910195561022221E06819961
chr1910259091029005E06826314
chr19983831985184E069-14411
chr1910195561022221E06919961
chr1910259091029005E06926314
chr19983831985184E070-14411
chr1910195561022221E07019961
chr19983831985184E071-14411
chr1910195561022221E07119961
chr1910259091029005E07126314
chr19983831985184E072-14411
chr1910195561022221E07219961
chr1910259091029005E07226314
chr19983831985184E073-14411
chr1910195561022221E07319961
chr1910259091029005E07326314
chr19983831985184E074-14411
chr1910195561022221E07419961
chr1910259091029005E07426314
chr1910195561022221E08119961
chr19983831985184E082-14411
chr1910001181000408E082523
chr1910195561022221E08219961
chr1910259091029005E08226314