rs1671152

Homo sapiens
T>G
GP6 : Missense Variant
LOC107985325 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0153 (18172/118550,ExAC)
T==0178 (5313/29776,GnomAD)
T==0222 (6478/29118,TOPMED)
G=0202 (2469/12202,GO-ESP)
T==0177 (886/5008,1000G)
T==0157 (604/3854,ALSPAC)
T==0154 (570/3708,TWINSUK)
chr19:55014977 (GRCh38.p7) (19q13.42)
CD
GWASdb2
6   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.55014977T>G
GRCh37.p13 chr 19 fix patch HG1079_PATCHNW_004166865.1:g.989345T>G
GP6 RefSeqGene LRG_560
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF2_CTG3_1NW_003571061.2:g.727138T>G
GRCh37.p13 chr 19 novel patch HSCHR19LRC_PGF2_CTG1NW_003571061.1:g.727137T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_T_CTG3_1NW_003571059.2:g.933342T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_S_CTG3_1NW_003571058.2:g.997049T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_J_CTG3_1NW_003571057.2:g.1022500T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_I_CTG3_1NW_003571056.2:g.994963T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX2_CTG3_1NW_003571055.2:g.660179T>G
GRCh37.p13 chr 19 novel patch HSCHR19LRC_COX2_CTG1NW_003571055.1:g.660178T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1NW_003571060.1:g.917759T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1NW_003571054.1:g.918375T>G
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1NT_187693.1:g.997459T>G
GRCh37.p13 chr 19NC_000019.9:g.55526345T>G

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.968A>CK [AAA]> T [ACA]Coding Sequence Variant
platelet glycoprotein VI isoform 1 precursorNP_001077368.2:p....NP_001077368.2:p.Lys323ThrK [Lys]> T [Thr]Missense Variant
GP6 transcript variant 3NM_001256017.2:c....NM_001256017.2:c.910A>CN [AAC]> H [CAC]Coding Sequence Variant
platelet glycoprotein VI isoform 3 precursorNP_001242946.2:p....NP_001242946.2:p.Asn304HisN [Asn]> H [His]Missense Variant
GP6 transcript variant 2NM_016363.5:c.964A>CN [AAC]> H [CAC]Coding Sequence Variant
platelet glycoprotein VI isoform 2 precursorNP_057447.5:p.Asn...NP_057447.5:p.Asn322HisN [Asn]> H [His]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
1000GenomesAfricanSub1322T=0.333G=0.667
1000GenomesAmericanSub694T=0.080G=0.920
1000GenomesEast AsianSub1008T=0.033G=0.967
1000GenomesEuropeSub1006T=0.141G=0.859
1000GenomesGlobalStudy-wide5008T=0.177G=0.823
1000GenomesSouth AsianSub978T=0.220G=0.780
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.157G=0.843
The Exome Aggregation ConsortiumAmericanSub20850T=0.176G=0.823
The Exome Aggregation ConsortiumAsianSub24782T=0.142G=0.857
The Exome Aggregation ConsortiumEuropeSub72042T=0.150G=0.849
The Exome Aggregation ConsortiumGlobalStudy-wide118550T=0.153G=0.846
The Exome Aggregation ConsortiumOtherSub876T=0.120G=0.880
The Genome Aggregation DatabaseAfricanSub8668T=0.302G=0.698
The Genome Aggregation DatabaseAmericanSub830T=0.100G=0.900
The Genome Aggregation DatabaseEast AsianSub1620T=0.019G=0.981
The Genome Aggregation DatabaseEuropeSub18356T=0.136G=0.863
The Genome Aggregation DatabaseGlobalStudy-wide29776T=0.178G=0.821
The Genome Aggregation DatabaseOtherSub302T=0.250G=0.750
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.222G=0.777
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.154G=0.846
PMID Title Author Journal
26308704Genetic variations of the GP6 regulatory region in patients with sticky platelet syndrome and miscarriage.Sokol JExpert Rev Hematol
20526338Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists.Johnson ADNat Genet
23958962Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.Gelernter JMol Psychiatry
21854539Genetic determinants of platelet reactivity during acetylsalicylic acid therapy in diabetic patients: evaluation of 27 polymorphisms within candidate genes.Postula MJ Thromb Haemost
25897256Personalized antiplatelet and anticoagulation therapy: applications and significance of pharmacogenomics.Beitelshees ALPharmgenomics Pers Med
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
rs16711520.0000567cocaine dependence23958962
rs16711520.000225cocaine dependence23958962
rs16711520.000515cocaine dependence,AA23958962
rs16711520.000884cocaine dependence23958962

eQTL of rs1671152 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr19:55526345GP6ENSG00000088053.7T>G9.0091e-6-23287Cerebellum
Chr19:55526345GP6ENSG00000088053.7T>G1.2367e-4-23287Cerebellar_Hemisphere

meQTL of rs1671152 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 )
chr19940207940264E067-49081
chr19950706950795E067-38550
chr19983359983479E067-5866
chr19983553983756E067-5589
chr1910156081015844E06726263
chr1910158511016391E06726506
chr1910164891017758E06727144
chr1910177871017841E06728442
chr1910178421017926E06728497
chr1910180581018350E06728713
chr1910184261018691E06729081
chr1910187601018893E06729415
chr19941664941993E068-47352
chr19983359983479E068-5866
chr19983553983756E068-5589
chr1910156081015844E06826263
chr1910158511016391E06826506
chr1910164891017758E06827144
chr1910177871017841E06828442
chr1910178421017926E06828497
chr1910180581018350E06828713
chr1910184261018691E06829081
chr1910187601018893E06829415
chr19941664941993E069-47352
chr19983359983479E069-5866
chr19983553983756E069-5589
chr19995473995566E0696128
chr1910158511016391E06926506
chr1910164891017758E06927144
chr1910177871017841E06928442
chr1910178421017926E06928497
chr1910180581018350E06928713
chr1910184261018691E06929081
chr1910187601018893E06929415
chr19940207940264E070-49081
chr19941664941993E070-47352
chr19942242942572E070-46773
chr19942585942669E070-46676
chr19944845945548E070-43797
chr19955812957516E070-31829
chr19983359983479E070-5866
chr19983553983756E070-5589
chr19985442985779E070-3566
chr19985854986068E070-3277
chr1910156081015844E07026263
chr1910158511016391E07026506
chr1910164891017758E07027144
chr1910177871017841E07028442
chr1910178421017926E07028497
chr1910180581018350E07028713
chr1910184261018691E07029081
chr1910187601018893E07029415
chr19940207940264E071-49081
chr19941664941993E071-47352
chr19983359983479E071-5866
chr19983553983756E071-5589
chr1910156081015844E07126263
chr1910158511016391E07126506
chr1910164891017758E07127144
chr1910177871017841E07128442
chr1910178421017926E07128497
chr1910180581018350E07128713
chr1910184261018691E07129081
chr1910187601018893E07129415
chr19941664941993E072-47352
chr19983359983479E072-5866
chr19983553983756E072-5589
chr1910158511016391E07226506
chr1910164891017758E07227144
chr1910177871017841E07228442
chr1910178421017926E07228497
chr1910180581018350E07228713
chr1910184261018691E07229081
chr1910187601018893E07229415
chr1910156081015844E07326263
chr1910158511016391E07326506
chr1910164891017758E07327144
chr1910177871017841E07328442
chr1910178421017926E07328497
chr1910180581018350E07328713
chr1910184261018691E07329081
chr1910187601018893E07329415
chr19941664941993E074-47352
chr19983359983479E074-5866
chr19983553983756E074-5589
chr1910158511016391E07426506
chr1910164891017758E07427144
chr1910177871017841E07428442
chr1910178421017926E07428497
chr1910180581018350E07428713
chr1910184261018691E07429081
chr1910187601018893E07429415
chr19940207940264E081-49081
chr19941664941993E081-47352
chr19983359983479E081-5866
chr19983553983756E081-5589
chr19985276985326E081-4019
chr19985442985779E081-3566
chr1910164891017758E08127144
chr1910177871017841E08128442
chr1910178421017926E08128497
chr1910180581018350E08128713
chr1910184261018691E08129081
chr1910187601018893E08129415
chr19940207940264E082-49081
chr19941664941993E082-47352
chr19944845945548E082-43797
chr19985276985326E082-4019
chr19985442985779E082-3566
chr19985854986068E082-3277
chr19986132986303E082-3042
chr19986710986821E082-2524
chr1910158511016391E08226506
chr1910164891017758E08227144
chr1910177871017841E08228442
chr1910178421017926E08228497
chr1910180581018350E08228713
chr1910184261018691E08229081
chr1910187601018893E08229415










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr19983831985184E067-4161
chr1910195561022221E06730211
chr1910259091029005E06736564
chr19983831985184E068-4161
chr1910195561022221E06830211
chr1910259091029005E06836564
chr19983831985184E069-4161
chr1910195561022221E06930211
chr1910259091029005E06936564
chr19983831985184E070-4161
chr1910195561022221E07030211
chr19983831985184E071-4161
chr1910195561022221E07130211
chr1910259091029005E07136564
chr19983831985184E072-4161
chr1910195561022221E07230211
chr1910259091029005E07236564
chr19983831985184E073-4161
chr1910195561022221E07330211
chr1910259091029005E07336564
chr19983831985184E074-4161
chr1910195561022221E07430211
chr1910259091029005E07436564
chr1910195561022221E08130211
chr19983831985184E082-4161
chr1910001181000408E08210773
chr1910195561022221E08230211
chr1910259091029005E08236564