rs1671151

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

GP6 : Synonymous Variant
LOC107985325 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0209 (25303/120710,ExAC)
G==0245 (7346/29936,GnomAD)
G==0314 (9149/29118,TOPMED)
A=0266 (3262/12250,GO-ESP)
G==0282 (1414/5008,1000G)
G==0183 (705/3854,ALSPAC)
G==0179 (663/3708,TWINSUK)

Position: chr19:55014526 (GRCh38.p7) (19q13.42)

Phenotype: CD

Dataset:

GWASdb2

Publications: 2 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.55014526G>A
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.988894G>A
GP6 RefSeqGene	LRG_560
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF2_CTG3_1	NW_003571061.2:g.726687G>A
GRCh37.p13 chr 19 novel patch HSCHR19LRC_PGF2_CTG1	NW_003571061.1:g.726686G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_T_CTG3_1	NW_003571059.2:g.932891G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_S_CTG3_1	NW_003571058.2:g.996598G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_J_CTG3_1	NW_003571057.2:g.1022049G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_I_CTG3_1	NW_003571056.2:g.994512G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX2_CTG3_1	NW_003571055.2:g.659728G>A
GRCh37.p13 chr 19 novel patch HSCHR19LRC_COX2_CTG1	NW_003571055.1:g.659727G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.917308G>A
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1	NW_003571054.1:g.917924G>A
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.997008G>A
GRCh37.p13 chr 19	NC_000019.9:g.55525894G>A

Gene: GP6, glycoprotein VI platelet(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GP6 transcript variant 3	NM_001256017.2:c.	N/A	3 Prime UTR Variant
GP6 transcript variant 2	NM_016363.5:c.	N/A	3 Prime UTR Variant
GP6 transcript variant 1	NM_001083899.2:c....NM_001083899.2:c.1419C>T	P [CCC]> P [CCT]	Coding Sequence Variant
platelet glycoprotein VI isoform 1 precursor	NP_001077368.2:p....NP_001077368.2:p.Pro473=	P [Pro]> P [Pro]	Synonymous 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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.501	A=0.499
1000Genomes	American	Sub	694	G=0.180	A=0.820
1000Genomes	East Asian	Sub	1008	G=0.188	A=0.812
1000Genomes	Europe	Sub	1006	G=0.154	A=0.846
1000Genomes	Global	Study-wide	5008	G=0.282	A=0.718
1000Genomes	South Asian	Sub	978	G=0.290	A=0.710
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.183	A=0.817
The Exome Aggregation Consortium	American	Sub	21364	G=0.310	A=0.689
The Exome Aggregation Consortium	Asian	Sub	25120	G=0.236	A=0.763
The Exome Aggregation Consortium	Europe	Sub	73326	G=0.171	A=0.828
The Exome Aggregation Consortium	Global	Study-wide	120710	G=0.209	A=0.790
The Exome Aggregation Consortium	Other	Sub	900	G=0.170	A=0.830
The Genome Aggregation Database	African	Sub	8704	G=0.466	A=0.534
The Genome Aggregation Database	American	Sub	838	G=0.170	A=0.830
The Genome Aggregation Database	East Asian	Sub	1620	G=0.150	A=0.850
The Genome Aggregation Database	Europe	Sub	18472	G=0.152	A=0.847
The Genome Aggregation Database	Global	Study-wide	29936	G=0.245	A=0.754
The Genome Aggregation Database	Other	Sub	302	G=0.260	A=0.740
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.314	A=0.685
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.179	A=0.821

PMID	Title	Author	Journal
23958962	Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.	Gelernter J	Mol Psychiatry
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

P-Value

SNP ID	p-value	Traits	Study
rs1671151	0.00028	cocaine dependence,AA	23958962
rs1671151	0.000562	cocaine dependence	23958962

eQTL of rs1671151 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:55525894	GP6	ENSG00000088053.7	G>A	9.0091e-6	-23738	Cerebellum
Chr19:55525894	GP6	ENSG00000088053.7	G>A	1.2367e-4	-23738	Cerebellar_Hemisphere

meQTL of rs1671151 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 )
chr19	940207	940264	E067	-48630
chr19	950706	950795	E067	-38099
chr19	983359	983479	E067	-5415
chr19	983553	983756	E067	-5138
chr19	1015608	1015844	E067	26714
chr19	1015851	1016391	E067	26957
chr19	1016489	1017758	E067	27595
chr19	1017787	1017841	E067	28893
chr19	1017842	1017926	E067	28948
chr19	1018058	1018350	E067	29164
chr19	1018426	1018691	E067	29532
chr19	1018760	1018893	E067	29866
chr19	941664	941993	E068	-46901
chr19	983359	983479	E068	-5415
chr19	983553	983756	E068	-5138
chr19	1015608	1015844	E068	26714
chr19	1015851	1016391	E068	26957
chr19	1016489	1017758	E068	27595
chr19	1017787	1017841	E068	28893
chr19	1017842	1017926	E068	28948
chr19	1018058	1018350	E068	29164
chr19	1018426	1018691	E068	29532
chr19	1018760	1018893	E068	29866
chr19	941664	941993	E069	-46901
chr19	983359	983479	E069	-5415
chr19	983553	983756	E069	-5138
chr19	995473	995566	E069	6579
chr19	1015851	1016391	E069	26957
chr19	1016489	1017758	E069	27595
chr19	1017787	1017841	E069	28893
chr19	1017842	1017926	E069	28948
chr19	1018058	1018350	E069	29164
chr19	1018426	1018691	E069	29532
chr19	1018760	1018893	E069	29866
chr19	940207	940264	E070	-48630
chr19	941664	941993	E070	-46901
chr19	942242	942572	E070	-46322
chr19	942585	942669	E070	-46225
chr19	944845	945548	E070	-43346
chr19	955812	957516	E070	-31378
chr19	983359	983479	E070	-5415
chr19	983553	983756	E070	-5138
chr19	985442	985779	E070	-3115
chr19	985854	986068	E070	-2826
chr19	1015608	1015844	E070	26714
chr19	1015851	1016391	E070	26957
chr19	1016489	1017758	E070	27595
chr19	1017787	1017841	E070	28893
chr19	1017842	1017926	E070	28948
chr19	1018058	1018350	E070	29164
chr19	1018426	1018691	E070	29532
chr19	1018760	1018893	E070	29866
chr19	940207	940264	E071	-48630
chr19	941664	941993	E071	-46901
chr19	983359	983479	E071	-5415
chr19	983553	983756	E071	-5138
chr19	1015608	1015844	E071	26714
chr19	1015851	1016391	E071	26957
chr19	1016489	1017758	E071	27595
chr19	1017787	1017841	E071	28893
chr19	1017842	1017926	E071	28948
chr19	1018058	1018350	E071	29164
chr19	1018426	1018691	E071	29532
chr19	1018760	1018893	E071	29866
chr19	941664	941993	E072	-46901
chr19	983359	983479	E072	-5415
chr19	983553	983756	E072	-5138
chr19	1015851	1016391	E072	26957
chr19	1016489	1017758	E072	27595
chr19	1017787	1017841	E072	28893
chr19	1017842	1017926	E072	28948
chr19	1018058	1018350	E072	29164
chr19	1018426	1018691	E072	29532
chr19	1018760	1018893	E072	29866
chr19	1015608	1015844	E073	26714
chr19	1015851	1016391	E073	26957
chr19	1016489	1017758	E073	27595
chr19	1017787	1017841	E073	28893
chr19	1017842	1017926	E073	28948
chr19	1018058	1018350	E073	29164
chr19	1018426	1018691	E073	29532
chr19	1018760	1018893	E073	29866
chr19	941664	941993	E074	-46901
chr19	983359	983479	E074	-5415
chr19	983553	983756	E074	-5138
chr19	1015851	1016391	E074	26957
chr19	1016489	1017758	E074	27595
chr19	1017787	1017841	E074	28893
chr19	1017842	1017926	E074	28948
chr19	1018058	1018350	E074	29164
chr19	1018426	1018691	E074	29532
chr19	1018760	1018893	E074	29866
chr19	940207	940264	E081	-48630
chr19	941664	941993	E081	-46901
chr19	983359	983479	E081	-5415
chr19	983553	983756	E081	-5138
chr19	985276	985326	E081	-3568
chr19	985442	985779	E081	-3115
chr19	1016489	1017758	E081	27595
chr19	1017787	1017841	E081	28893
chr19	1017842	1017926	E081	28948
chr19	1018058	1018350	E081	29164
chr19	1018426	1018691	E081	29532
chr19	1018760	1018893	E081	29866
chr19	940207	940264	E082	-48630
chr19	941664	941993	E082	-46901
chr19	944845	945548	E082	-43346
chr19	985276	985326	E082	-3568
chr19	985442	985779	E082	-3115
chr19	985854	986068	E082	-2826
chr19	986132	986303	E082	-2591
chr19	986710	986821	E082	-2073
chr19	1015851	1016391	E082	26957
chr19	1016489	1017758	E082	27595
chr19	1017787	1017841	E082	28893
chr19	1017842	1017926	E082	28948
chr19	1018058	1018350	E082	29164
chr19	1018426	1018691	E082	29532
chr19	1018760	1018893	E082	29866

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	983831	985184	E067	-3710
chr19	1019556	1022221	E067	30662
chr19	1025909	1029005	E067	37015
chr19	983831	985184	E068	-3710
chr19	1019556	1022221	E068	30662
chr19	1025909	1029005	E068	37015
chr19	983831	985184	E069	-3710
chr19	1019556	1022221	E069	30662
chr19	1025909	1029005	E069	37015
chr19	983831	985184	E070	-3710
chr19	1019556	1022221	E070	30662
chr19	983831	985184	E071	-3710
chr19	1019556	1022221	E071	30662
chr19	1025909	1029005	E071	37015
chr19	983831	985184	E072	-3710
chr19	1019556	1022221	E072	30662
chr19	1025909	1029005	E072	37015
chr19	983831	985184	E073	-3710
chr19	1019556	1022221	E073	30662
chr19	1025909	1029005	E073	37015
chr19	983831	985184	E074	-3710
chr19	1019556	1022221	E074	30662
chr19	1025909	1029005	E074	37015
chr19	1019556	1022221	E081	30662
chr19	983831	985184	E082	-3710
chr19	1000118	1000408	E082	11224
chr19	1019556	1022221	E082	30662
chr19	1025909	1029005	E082	37015