rs2304167

Homo sapiens
C>T
GP6 : Missense Variant
LOC107985325 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0210 (25291/120120,ExAC)
C==0248 (7436/29872,GnomAD)
C==0318 (9282/29118,TOPMED)
T=0269 (3326/12362,GO-ESP)
C==0287 (1435/5008,1000G)
C==0183 (707/3854,ALSPAC)
C==0179 (665/3708,TWINSUK)
chr19:55015713 (GRCh38.p7) (19q13.42)
CD
GWASdb2
3   publication(s)
See rs on genome
119 Enhancers around
28 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 19NC_000019.10:g.55015713C>T
GRCh37.p13 chr 19 fix patch HG1079_PATCHNW_004166865.1:g.990081C>T
GP6 RefSeqGene LRG_560
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF2_CTG3_1NW_003571061.2:g.727874C>T
GRCh37.p13 chr 19 novel patch HSCHR19LRC_PGF2_CTG1NW_003571061.1:g.727873C>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_T_CTG3_1NW_003571059.2:g.934078C>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_S_CTG3_1NW_003571058.2:g.997785C>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_J_CTG3_1NW_003571057.2:g.1023236C>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_I_CTG3_1NW_003571056.2:g.995699C>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX2_CTG3_1NW_003571055.2:g.660915C>T
GRCh37.p13 chr 19 novel patch HSCHR19LRC_COX2_CTG1NW_003571055.1:g.660914C>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1NW_003571060.1:g.918495C>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1NW_003571054.1:g.919111C>T
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1NT_187693.1:g.998195C>T
GRCh37.p13 chr 19NC_000019.9:g.55527081C>T

Gene: GP6, glycoprotein VI platelet(minus strand)

Molecule type Change Amino acid[Codon] SO Term
GP6 transcript variant 1NM_001083899.2:c....NM_001083899.2:c.745G>AA [GCC]> T [ACC]Coding Sequence Variant
platelet glycoprotein VI isoform 1 precursorNP_001077368.2:p....NP_001077368.2:p.Ala249ThrA [Ala]> T [Thr]Missense Variant
GP6 transcript variant 3NM_001256017.2:c....NM_001256017.2:c.691G>AA [GCC]> T [ACC]Coding Sequence Variant
platelet glycoprotein VI isoform 3 precursorNP_001242946.2:p....NP_001242946.2:p.Ala231ThrA [Ala]> T [Thr]Missense Variant
GP6 transcript variant 2NM_016363.5:c.745G>AA [GCC]> T [ACC]Coding Sequence Variant
platelet glycoprotein VI isoform 2 precursorNP_057447.5:p.Ala...NP_057447.5:p.Ala249ThrA [Ala]> T [Thr]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
1000GenomesAfricanSub1322C=0.514T=0.486
1000GenomesAmericanSub694C=0.180T=0.820
1000GenomesEast AsianSub1008C=0.189T=0.811
1000GenomesEuropeSub1006C=0.154T=0.846
1000GenomesGlobalStudy-wide5008C=0.287T=0.713
1000GenomesSouth AsianSub978C=0.290T=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.183T=0.817
The Exome Aggregation ConsortiumAmericanSub21246C=0.315T=0.684
The Exome Aggregation ConsortiumAsianSub24952C=0.236T=0.763
The Exome Aggregation ConsortiumEuropeSub73030C=0.171T=0.828
The Exome Aggregation ConsortiumGlobalStudy-wide120120C=0.210T=0.789
The Exome Aggregation ConsortiumOtherSub892C=0.170T=0.830
The Genome Aggregation DatabaseAfricanSub8676C=0.480T=0.520
The Genome Aggregation DatabaseAmericanSub836C=0.170T=0.830
The Genome Aggregation DatabaseEast AsianSub1616C=0.151T=0.849
The Genome Aggregation DatabaseEuropeSub18442C=0.151T=0.848
The Genome Aggregation DatabaseGlobalStudy-wide29872C=0.248T=0.751
The Genome Aggregation DatabaseOtherSub302C=0.260T=0.740
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.318T=0.681
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.179T=0.821
PMID Title Author Journal
20227257Polymorphisms in the platelet-specific collagen receptor GP6 are associated with risk of nonfatal myocardial infarction in Caucasians.Shaffer JRNutr Metab Cardiovasc Dis
23958962Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.Gelernter JMol Psychiatry
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

P-Value

SNP ID p-value Traits Study
rs23041670.0000844cocaine dependence,AA23958962
rs23041670.000209cocaine dependence23958962

eQTL of rs2304167 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr19:55527081GP6ENSG00000088053.7C>T9.0091e-6-22551Cerebellum
Chr19:55527081GP6ENSG00000088053.7C>T1.2367e-4-22551Cerebellar_Hemisphere

meQTL of rs2304167 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 )
chr19940207940264E067-49817
chr19950706950795E067-39286
chr19983359983479E067-6602
chr19983553983756E067-6325
chr1910156081015844E06725527
chr1910158511016391E06725770
chr1910164891017758E06726408
chr1910177871017841E06727706
chr1910178421017926E06727761
chr1910180581018350E06727977
chr1910184261018691E06728345
chr1910187601018893E06728679
chr19941664941993E068-48088
chr19983359983479E068-6602
chr19983553983756E068-6325
chr1910156081015844E06825527
chr1910158511016391E06825770
chr1910164891017758E06826408
chr1910177871017841E06827706
chr1910178421017926E06827761
chr1910180581018350E06827977
chr1910184261018691E06828345
chr1910187601018893E06828679
chr19941664941993E069-48088
chr19983359983479E069-6602
chr19983553983756E069-6325
chr19995473995566E0695392
chr1910158511016391E06925770
chr1910164891017758E06926408
chr1910177871017841E06927706
chr1910178421017926E06927761
chr1910180581018350E06927977
chr1910184261018691E06928345
chr1910187601018893E06928679
chr19940207940264E070-49817
chr19941664941993E070-48088
chr19942242942572E070-47509
chr19942585942669E070-47412
chr19944845945548E070-44533
chr19955812957516E070-32565
chr19983359983479E070-6602
chr19983553983756E070-6325
chr19985442985779E070-4302
chr19985854986068E070-4013
chr1910156081015844E07025527
chr1910158511016391E07025770
chr1910164891017758E07026408
chr1910177871017841E07027706
chr1910178421017926E07027761
chr1910180581018350E07027977
chr1910184261018691E07028345
chr1910187601018893E07028679
chr19940207940264E071-49817
chr19941664941993E071-48088
chr19983359983479E071-6602
chr19983553983756E071-6325
chr1910156081015844E07125527
chr1910158511016391E07125770
chr1910164891017758E07126408
chr1910177871017841E07127706
chr1910178421017926E07127761
chr1910180581018350E07127977
chr1910184261018691E07128345
chr1910187601018893E07128679
chr19941664941993E072-48088
chr19983359983479E072-6602
chr19983553983756E072-6325
chr1910158511016391E07225770
chr1910164891017758E07226408
chr1910177871017841E07227706
chr1910178421017926E07227761
chr1910180581018350E07227977
chr1910184261018691E07228345
chr1910187601018893E07228679
chr1910156081015844E07325527
chr1910158511016391E07325770
chr1910164891017758E07326408
chr1910177871017841E07327706
chr1910178421017926E07327761
chr1910180581018350E07327977
chr1910184261018691E07328345
chr1910187601018893E07328679
chr19941664941993E074-48088
chr19983359983479E074-6602
chr19983553983756E074-6325
chr1910158511016391E07425770
chr1910164891017758E07426408
chr1910177871017841E07427706
chr1910178421017926E07427761
chr1910180581018350E07427977
chr1910184261018691E07428345
chr1910187601018893E07428679
chr19940207940264E081-49817
chr19941664941993E081-48088
chr19983359983479E081-6602
chr19983553983756E081-6325
chr19985276985326E081-4755
chr19985442985779E081-4302
chr1910164891017758E08126408
chr1910177871017841E08127706
chr1910178421017926E08127761
chr1910180581018350E08127977
chr1910184261018691E08128345
chr1910187601018893E08128679
chr19940207940264E082-49817
chr19941664941993E082-48088
chr19944845945548E082-44533
chr19985276985326E082-4755
chr19985442985779E082-4302
chr19985854986068E082-4013
chr19986132986303E082-3778
chr19986710986821E082-3260
chr1910158511016391E08225770
chr1910164891017758E08226408
chr1910177871017841E08227706
chr1910178421017926E08227761
chr1910180581018350E08227977
chr1910184261018691E08228345
chr1910187601018893E08228679










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr19983831985184E067-4897
chr1910195561022221E06729475
chr1910259091029005E06735828
chr19983831985184E068-4897
chr1910195561022221E06829475
chr1910259091029005E06835828
chr19983831985184E069-4897
chr1910195561022221E06929475
chr1910259091029005E06935828
chr19983831985184E070-4897
chr1910195561022221E07029475
chr19983831985184E071-4897
chr1910195561022221E07129475
chr1910259091029005E07135828
chr19983831985184E072-4897
chr1910195561022221E07229475
chr1910259091029005E07235828
chr19983831985184E073-4897
chr1910195561022221E07329475
chr1910259091029005E07335828
chr19983831985184E074-4897
chr1910195561022221E07429475
chr1910259091029005E07435828
chr1910195561022221E08129475
chr19983831985184E082-4897
chr1910001181000408E08210037
chr1910195561022221E08229475
chr1910259091029005E08235828