rs1671152

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

GP6 : Missense Variant
LOC107985325 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

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)

Position: chr19:55014977 (GRCh38.p7) (19q13.42)

Phenotype: CD

Dataset:

GWASdb2

Publications: 6 publication(s)

Genomic View: See rs on genome

Enhancer: 119 Enhancers around

Promoter: 28 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.55014977T>G
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.989345T>G
GP6 RefSeqGene	LRG_560
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF2_CTG3_1	NW_003571061.2:g.727138T>G
GRCh37.p13 chr 19 novel patch HSCHR19LRC_PGF2_CTG1	NW_003571061.1:g.727137T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_T_CTG3_1	NW_003571059.2:g.933342T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_S_CTG3_1	NW_003571058.2:g.997049T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_J_CTG3_1	NW_003571057.2:g.1022500T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_I_CTG3_1	NW_003571056.2:g.994963T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX2_CTG3_1	NW_003571055.2:g.660179T>G
GRCh37.p13 chr 19 novel patch HSCHR19LRC_COX2_CTG1	NW_003571055.1:g.660178T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.917759T>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1	NW_003571054.1:g.918375T>G
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.997459T>G
GRCh37.p13 chr 19	NC_000019.9:g.55526345T>G

Gene: GP6, glycoprotein VI platelet(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GP6 transcript variant 1	NM_001083899.2:c....NM_001083899.2:c.968A>C	K [AAA]> T [ACA]	Coding Sequence Variant
platelet glycoprotein VI isoform 1 precursor	NP_001077368.2:p....NP_001077368.2:p.Lys323Thr	K [Lys]> T [Thr]	Missense Variant
GP6 transcript variant 3	NM_001256017.2:c....NM_001256017.2:c.910A>C	N [AAC]> H [CAC]	Coding Sequence Variant
platelet glycoprotein VI isoform 3 precursor	NP_001242946.2:p....NP_001242946.2:p.Asn304His	N [Asn]> H [His]	Missense Variant
GP6 transcript variant 2	NM_016363.5:c.964A>C	N [AAC]> H [CAC]	Coding Sequence Variant
platelet glycoprotein VI isoform 2 precursor	NP_057447.5:p.Asn...NP_057447.5:p.Asn322His	N [Asn]> H [His]	Missense Variant

Gene: LOC107985325, uncharacterized LOC107985325(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985325 transcript variant X1	XR_001754012.1:n.	N/A	Intron Variant
LOC107985325 transcript variant X2	XR_001754013.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.333	G=0.667
1000Genomes	American	Sub	694	T=0.080	G=0.920
1000Genomes	East Asian	Sub	1008	T=0.033	G=0.967
1000Genomes	Europe	Sub	1006	T=0.141	G=0.859
1000Genomes	Global	Study-wide	5008	T=0.177	G=0.823
1000Genomes	South Asian	Sub	978	T=0.220	G=0.780
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.157	G=0.843
The Exome Aggregation Consortium	American	Sub	20850	T=0.176	G=0.823
The Exome Aggregation Consortium	Asian	Sub	24782	T=0.142	G=0.857
The Exome Aggregation Consortium	Europe	Sub	72042	T=0.150	G=0.849
The Exome Aggregation Consortium	Global	Study-wide	118550	T=0.153	G=0.846
The Exome Aggregation Consortium	Other	Sub	876	T=0.120	G=0.880
The Genome Aggregation Database	African	Sub	8668	T=0.302	G=0.698
The Genome Aggregation Database	American	Sub	830	T=0.100	G=0.900
The Genome Aggregation Database	East Asian	Sub	1620	T=0.019	G=0.981
The Genome Aggregation Database	Europe	Sub	18356	T=0.136	G=0.863
The Genome Aggregation Database	Global	Study-wide	29776	T=0.178	G=0.821
The Genome Aggregation Database	Other	Sub	302	T=0.250	G=0.750
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.222	G=0.777
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.154	G=0.846

PMID	Title	Author	Journal
26308704	Genetic variations of the GP6 regulatory region in patients with sticky platelet syndrome and miscarriage.	Sokol J	Expert Rev Hematol
20526338	Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists.	Johnson AD	Nat Genet
23958962	Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.	Gelernter J	Mol Psychiatry
21854539	Genetic determinants of platelet reactivity during acetylsalicylic acid therapy in diabetic patients: evaluation of 27 polymorphisms within candidate genes.	Postula M	J Thromb Haemost
25897256	Personalized antiplatelet and anticoagulation therapy: applications and significance of pharmacogenomics.	Beitelshees AL	Pharmgenomics Pers Med
25741868	Standards 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 S	Genet Med

SNP ID	p-value	Traits	Study
rs1671152	0.0000567	cocaine dependence	23958962
rs1671152	0.000225	cocaine dependence	23958962
rs1671152	0.000515	cocaine dependence,AA	23958962
rs1671152	0.000884	cocaine dependence	23958962

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:55526345	GP6	ENSG00000088053.7	T>G	9.0091e-6	-23287	Cerebellum
Chr19:55526345	GP6	ENSG00000088053.7	T>G	1.2367e-4	-23287	Cerebellar_Hemisphere

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 )
chr19	940207	940264	E067	-49081
chr19	950706	950795	E067	-38550
chr19	983359	983479	E067	-5866
chr19	983553	983756	E067	-5589
chr19	1015608	1015844	E067	26263
chr19	1015851	1016391	E067	26506
chr19	1016489	1017758	E067	27144
chr19	1017787	1017841	E067	28442
chr19	1017842	1017926	E067	28497
chr19	1018058	1018350	E067	28713
chr19	1018426	1018691	E067	29081
chr19	1018760	1018893	E067	29415
chr19	941664	941993	E068	-47352
chr19	983359	983479	E068	-5866
chr19	983553	983756	E068	-5589
chr19	1015608	1015844	E068	26263
chr19	1015851	1016391	E068	26506
chr19	1016489	1017758	E068	27144
chr19	1017787	1017841	E068	28442
chr19	1017842	1017926	E068	28497
chr19	1018058	1018350	E068	28713
chr19	1018426	1018691	E068	29081
chr19	1018760	1018893	E068	29415
chr19	941664	941993	E069	-47352
chr19	983359	983479	E069	-5866
chr19	983553	983756	E069	-5589
chr19	995473	995566	E069	6128
chr19	1015851	1016391	E069	26506
chr19	1016489	1017758	E069	27144
chr19	1017787	1017841	E069	28442
chr19	1017842	1017926	E069	28497
chr19	1018058	1018350	E069	28713
chr19	1018426	1018691	E069	29081
chr19	1018760	1018893	E069	29415
chr19	940207	940264	E070	-49081
chr19	941664	941993	E070	-47352
chr19	942242	942572	E070	-46773
chr19	942585	942669	E070	-46676
chr19	944845	945548	E070	-43797
chr19	955812	957516	E070	-31829
chr19	983359	983479	E070	-5866
chr19	983553	983756	E070	-5589
chr19	985442	985779	E070	-3566
chr19	985854	986068	E070	-3277
chr19	1015608	1015844	E070	26263
chr19	1015851	1016391	E070	26506
chr19	1016489	1017758	E070	27144
chr19	1017787	1017841	E070	28442
chr19	1017842	1017926	E070	28497
chr19	1018058	1018350	E070	28713
chr19	1018426	1018691	E070	29081
chr19	1018760	1018893	E070	29415
chr19	940207	940264	E071	-49081
chr19	941664	941993	E071	-47352
chr19	983359	983479	E071	-5866
chr19	983553	983756	E071	-5589
chr19	1015608	1015844	E071	26263
chr19	1015851	1016391	E071	26506
chr19	1016489	1017758	E071	27144
chr19	1017787	1017841	E071	28442
chr19	1017842	1017926	E071	28497
chr19	1018058	1018350	E071	28713
chr19	1018426	1018691	E071	29081
chr19	1018760	1018893	E071	29415
chr19	941664	941993	E072	-47352
chr19	983359	983479	E072	-5866
chr19	983553	983756	E072	-5589
chr19	1015851	1016391	E072	26506
chr19	1016489	1017758	E072	27144
chr19	1017787	1017841	E072	28442
chr19	1017842	1017926	E072	28497
chr19	1018058	1018350	E072	28713
chr19	1018426	1018691	E072	29081
chr19	1018760	1018893	E072	29415
chr19	1015608	1015844	E073	26263
chr19	1015851	1016391	E073	26506
chr19	1016489	1017758	E073	27144
chr19	1017787	1017841	E073	28442
chr19	1017842	1017926	E073	28497
chr19	1018058	1018350	E073	28713
chr19	1018426	1018691	E073	29081
chr19	1018760	1018893	E073	29415
chr19	941664	941993	E074	-47352
chr19	983359	983479	E074	-5866
chr19	983553	983756	E074	-5589
chr19	1015851	1016391	E074	26506
chr19	1016489	1017758	E074	27144
chr19	1017787	1017841	E074	28442
chr19	1017842	1017926	E074	28497
chr19	1018058	1018350	E074	28713
chr19	1018426	1018691	E074	29081
chr19	1018760	1018893	E074	29415
chr19	940207	940264	E081	-49081
chr19	941664	941993	E081	-47352
chr19	983359	983479	E081	-5866
chr19	983553	983756	E081	-5589
chr19	985276	985326	E081	-4019
chr19	985442	985779	E081	-3566
chr19	1016489	1017758	E081	27144
chr19	1017787	1017841	E081	28442
chr19	1017842	1017926	E081	28497
chr19	1018058	1018350	E081	28713
chr19	1018426	1018691	E081	29081
chr19	1018760	1018893	E081	29415
chr19	940207	940264	E082	-49081
chr19	941664	941993	E082	-47352
chr19	944845	945548	E082	-43797
chr19	985276	985326	E082	-4019
chr19	985442	985779	E082	-3566
chr19	985854	986068	E082	-3277
chr19	986132	986303	E082	-3042
chr19	986710	986821	E082	-2524
chr19	1015851	1016391	E082	26506
chr19	1016489	1017758	E082	27144
chr19	1017787	1017841	E082	28442
chr19	1017842	1017926	E082	28497
chr19	1018058	1018350	E082	28713
chr19	1018426	1018691	E082	29081
chr19	1018760	1018893	E082	29415

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	983831	985184	E067	-4161
chr19	1019556	1022221	E067	30211
chr19	1025909	1029005	E067	36564
chr19	983831	985184	E068	-4161
chr19	1019556	1022221	E068	30211
chr19	1025909	1029005	E068	36564
chr19	983831	985184	E069	-4161
chr19	1019556	1022221	E069	30211
chr19	1025909	1029005	E069	36564
chr19	983831	985184	E070	-4161
chr19	1019556	1022221	E070	30211
chr19	983831	985184	E071	-4161
chr19	1019556	1022221	E071	30211
chr19	1025909	1029005	E071	36564
chr19	983831	985184	E072	-4161
chr19	1019556	1022221	E072	30211
chr19	1025909	1029005	E072	36564
chr19	983831	985184	E073	-4161
chr19	1019556	1022221	E073	30211
chr19	1025909	1029005	E073	36564
chr19	983831	985184	E074	-4161
chr19	1019556	1022221	E074	30211
chr19	1025909	1029005	E074	36564
chr19	1019556	1022221	E081	30211
chr19	983831	985184	E082	-4161
chr19	1000118	1000408	E082	10773
chr19	1019556	1022221	E082	30211
chr19	1025909	1029005	E082	36564

rs1671152

Genomic Coordinates

Gene: GP6, glycoprotein VI platelet(minus strand)

Gene: LOC107985325, uncharacterized LOC107985325(plus strand)

Population Frequency

P-Value

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

meQTL of rs1671152 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)