rs1671150

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

GP6 : Missense Variant
LOC107985325 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0234 (7007/29922,GnomAD)
A==0298 (8679/29118,TOPMED)
A==0231 (2909/12592,ExAC)
G=0194 (1774/9130,GO-ESP)
A==0273 (1369/5008,1000G)
A==0183 (705/3854,ALSPAC)
A==0179 (663/3708,TWINSUK)

Position: chr19:55014129 (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.55014129A>G
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.988497A>G
GP6 RefSeqGene	LRG_560
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF2_CTG3_1	NW_003571061.2:g.726290A>G
GRCh37.p13 chr 19 novel patch HSCHR19LRC_PGF2_CTG1	NW_003571061.1:g.726289A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_T_CTG3_1	NW_003571059.2:g.932494A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_S_CTG3_1	NW_003571058.2:g.996201A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_J_CTG3_1	NW_003571057.2:g.1021652A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_I_CTG3_1	NW_003571056.2:g.994115A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX2_CTG3_1	NW_003571055.2:g.659331A>G
GRCh37.p13 chr 19 novel patch HSCHR19LRC_COX2_CTG1	NW_003571055.1:g.659330A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.916911A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1	NW_003571054.1:g.917527A>G
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.996611A>G
GRCh37.p13 chr 19	NC_000019.9:g.55525497A>G

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.1816T>C	F [TTT]> L [CTT]	Coding Sequence Variant
platelet glycoprotein VI isoform 1 precursor	NP_001077368.2:p....NP_001077368.2:p.Phe606Leu	F [Phe]> L [Leu]	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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.467	G=0.533
1000Genomes	American	Sub	694	A=0.180	G=0.820
1000Genomes	East Asian	Sub	1008	A=0.188	G=0.812
1000Genomes	Europe	Sub	1006	A=0.154	G=0.846
1000Genomes	Global	Study-wide	5008	A=0.273	G=0.727
1000Genomes	South Asian	Sub	978	A=0.290	G=0.710
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.183	G=0.817
The Exome Aggregation Consortium	American	Sub	648	A=0.290	G=0.710
The Exome Aggregation Consortium	Asian	Sub	7838	A=0.255	G=0.745
The Exome Aggregation Consortium	Europe	Sub	3964	A=0.174	G=0.826
The Exome Aggregation Consortium	Global	Study-wide	12592	A=0.231	G=0.769
The Exome Aggregation Consortium	Other	Sub	142	A=0.200	G=0.800
The Genome Aggregation Database	African	Sub	8704	A=0.429	G=0.571
The Genome Aggregation Database	American	Sub	838	A=0.170	G=0.830
The Genome Aggregation Database	East Asian	Sub	1612	A=0.150	G=0.850
The Genome Aggregation Database	Europe	Sub	18466	A=0.152	G=0.847
The Genome Aggregation Database	Global	Study-wide	29922	A=0.234	G=0.765
The Genome Aggregation Database	Other	Sub	302	A=0.260	G=0.740
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.298	G=0.701
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.179	G=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
rs1671150	0.000147	cocaine dependence,AA	23958962
rs1671150	0.000476	cocaine dependence	23958962

eQTL of rs1671150 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:55525497	GP6	ENSG00000088053.7	A>G	9.0091e-6	-24135	Cerebellum
Chr19:55525497	GP6	ENSG00000088053.7	A>G	1.2367e-4	-24135	Cerebellar_Hemisphere

meQTL of rs1671150 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	-48233
chr19	950706	950795	E067	-37702
chr19	983359	983479	E067	-5018
chr19	983553	983756	E067	-4741
chr19	1015608	1015844	E067	27111
chr19	1015851	1016391	E067	27354
chr19	1016489	1017758	E067	27992
chr19	1017787	1017841	E067	29290
chr19	1017842	1017926	E067	29345
chr19	1018058	1018350	E067	29561
chr19	1018426	1018691	E067	29929
chr19	1018760	1018893	E067	30263
chr19	941664	941993	E068	-46504
chr19	983359	983479	E068	-5018
chr19	983553	983756	E068	-4741
chr19	1015608	1015844	E068	27111
chr19	1015851	1016391	E068	27354
chr19	1016489	1017758	E068	27992
chr19	1017787	1017841	E068	29290
chr19	1017842	1017926	E068	29345
chr19	1018058	1018350	E068	29561
chr19	1018426	1018691	E068	29929
chr19	1018760	1018893	E068	30263
chr19	941664	941993	E069	-46504
chr19	983359	983479	E069	-5018
chr19	983553	983756	E069	-4741
chr19	995473	995566	E069	6976
chr19	1015851	1016391	E069	27354
chr19	1016489	1017758	E069	27992
chr19	1017787	1017841	E069	29290
chr19	1017842	1017926	E069	29345
chr19	1018058	1018350	E069	29561
chr19	1018426	1018691	E069	29929
chr19	1018760	1018893	E069	30263
chr19	940207	940264	E070	-48233
chr19	941664	941993	E070	-46504
chr19	942242	942572	E070	-45925
chr19	942585	942669	E070	-45828
chr19	944845	945548	E070	-42949
chr19	955812	957516	E070	-30981
chr19	983359	983479	E070	-5018
chr19	983553	983756	E070	-4741
chr19	985442	985779	E070	-2718
chr19	985854	986068	E070	-2429
chr19	1015608	1015844	E070	27111
chr19	1015851	1016391	E070	27354
chr19	1016489	1017758	E070	27992
chr19	1017787	1017841	E070	29290
chr19	1017842	1017926	E070	29345
chr19	1018058	1018350	E070	29561
chr19	1018426	1018691	E070	29929
chr19	1018760	1018893	E070	30263
chr19	940207	940264	E071	-48233
chr19	941664	941993	E071	-46504
chr19	983359	983479	E071	-5018
chr19	983553	983756	E071	-4741
chr19	1015608	1015844	E071	27111
chr19	1015851	1016391	E071	27354
chr19	1016489	1017758	E071	27992
chr19	1017787	1017841	E071	29290
chr19	1017842	1017926	E071	29345
chr19	1018058	1018350	E071	29561
chr19	1018426	1018691	E071	29929
chr19	1018760	1018893	E071	30263
chr19	941664	941993	E072	-46504
chr19	983359	983479	E072	-5018
chr19	983553	983756	E072	-4741
chr19	1015851	1016391	E072	27354
chr19	1016489	1017758	E072	27992
chr19	1017787	1017841	E072	29290
chr19	1017842	1017926	E072	29345
chr19	1018058	1018350	E072	29561
chr19	1018426	1018691	E072	29929
chr19	1018760	1018893	E072	30263
chr19	1015608	1015844	E073	27111
chr19	1015851	1016391	E073	27354
chr19	1016489	1017758	E073	27992
chr19	1017787	1017841	E073	29290
chr19	1017842	1017926	E073	29345
chr19	1018058	1018350	E073	29561
chr19	1018426	1018691	E073	29929
chr19	1018760	1018893	E073	30263
chr19	941664	941993	E074	-46504
chr19	983359	983479	E074	-5018
chr19	983553	983756	E074	-4741
chr19	1015851	1016391	E074	27354
chr19	1016489	1017758	E074	27992
chr19	1017787	1017841	E074	29290
chr19	1017842	1017926	E074	29345
chr19	1018058	1018350	E074	29561
chr19	1018426	1018691	E074	29929
chr19	1018760	1018893	E074	30263
chr19	940207	940264	E081	-48233
chr19	941664	941993	E081	-46504
chr19	983359	983479	E081	-5018
chr19	983553	983756	E081	-4741
chr19	985276	985326	E081	-3171
chr19	985442	985779	E081	-2718
chr19	1016489	1017758	E081	27992
chr19	1017787	1017841	E081	29290
chr19	1017842	1017926	E081	29345
chr19	1018058	1018350	E081	29561
chr19	1018426	1018691	E081	29929
chr19	1018760	1018893	E081	30263
chr19	940207	940264	E082	-48233
chr19	941664	941993	E082	-46504
chr19	944845	945548	E082	-42949
chr19	985276	985326	E082	-3171
chr19	985442	985779	E082	-2718
chr19	985854	986068	E082	-2429
chr19	986132	986303	E082	-2194
chr19	986710	986821	E082	-1676
chr19	1015851	1016391	E082	27354
chr19	1016489	1017758	E082	27992
chr19	1017787	1017841	E082	29290
chr19	1017842	1017926	E082	29345
chr19	1018058	1018350	E082	29561
chr19	1018426	1018691	E082	29929
chr19	1018760	1018893	E082	30263

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	983831	985184	E067	-3313
chr19	1019556	1022221	E067	31059
chr19	1025909	1029005	E067	37412
chr19	983831	985184	E068	-3313
chr19	1019556	1022221	E068	31059
chr19	1025909	1029005	E068	37412
chr19	983831	985184	E069	-3313
chr19	1019556	1022221	E069	31059
chr19	1025909	1029005	E069	37412
chr19	983831	985184	E070	-3313
chr19	1019556	1022221	E070	31059
chr19	983831	985184	E071	-3313
chr19	1019556	1022221	E071	31059
chr19	1025909	1029005	E071	37412
chr19	983831	985184	E072	-3313
chr19	1019556	1022221	E072	31059
chr19	1025909	1029005	E072	37412
chr19	983831	985184	E073	-3313
chr19	1019556	1022221	E073	31059
chr19	1025909	1029005	E073	37412
chr19	983831	985184	E074	-3313
chr19	1019556	1022221	E074	31059
chr19	1025909	1029005	E074	37412
chr19	1019556	1022221	E081	31059
chr19	983831	985184	E082	-3313
chr19	1000118	1000408	E082	11621
chr19	1019556	1022221	E082	31059
chr19	1025909	1029005	E082	37412