rs1654413

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

GP6 : Missense Variant
LOC107985325 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0200 (23279/116280,ExAC)
A==0302 (8812/29118,TOPMED)
T=0255 (3079/12070,GO-ESP)
A==0275 (1378/5008,1000G)
A==0182 (702/3854,ALSPAC)
A==0174 (646/3708,TWINSUK)

Position: chr19:55014991 (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.55014991A>T
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.989359A>T
GP6 RefSeqGene	LRG_560
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF2_CTG3_1	NW_003571061.2:g.727152A>T
GRCh37.p13 chr 19 novel patch HSCHR19LRC_PGF2_CTG1	NW_003571061.1:g.727151A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_T_CTG3_1	NW_003571059.2:g.933356A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_S_CTG3_1	NW_003571058.2:g.997063A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_J_CTG3_1	NW_003571057.2:g.1022514A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_I_CTG3_1	NW_003571056.2:g.994977A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX2_CTG3_1	NW_003571055.2:g.660193A>T
GRCh37.p13 chr 19 novel patch HSCHR19LRC_COX2_CTG1	NW_003571055.1:g.660192A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.917773A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1	NW_003571054.1:g.918389A>T
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.997473A>T
GRCh37.p13 chr 19	NC_000019.9:g.55526359A>T

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.954T>A	A [GCT]> A [GCA]	Coding Sequence Variant
platelet glycoprotein VI isoform 1 precursor	NP_001077368.2:p....NP_001077368.2:p.Ala318=	A [Ala]> A [Ala]	Synonymous Variant
GP6 transcript variant 3	NM_001256017.2:c....NM_001256017.2:c.896T>A	L [CTG]> Q [CAG]	Coding Sequence Variant
platelet glycoprotein VI isoform 3 precursor	NP_001242946.2:p....NP_001242946.2:p.Leu299Gln	L [Leu]> Q [Gln]	Missense Variant
GP6 transcript variant 2	NM_016363.5:c.950T>A	L [CTG]> Q [CAG]	Coding Sequence Variant
platelet glycoprotein VI isoform 2 precursor	NP_057447.5:p.Leu...NP_057447.5:p.Leu317Gln	L [Leu]> Q [Gln]	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=0.474	T=0.526
1000Genomes	American	Sub	694	A=0.170	T=0.830
1000Genomes	East Asian	Sub	1008	A=0.187	T=0.813
1000Genomes	Europe	Sub	1006	A=0.157	T=0.843
1000Genomes	Global	Study-wide	5008	A=0.275	T=0.725
1000Genomes	South Asian	Sub	978	A=0.290	T=0.710
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.182	T=0.818
The Exome Aggregation Consortium	American	Sub	20170	A=0.280	T=0.719
The Exome Aggregation Consortium	Asian	Sub	24474	A=0.230	T=0.769
The Exome Aggregation Consortium	Europe	Sub	70764	A=0.167	T=0.832
The Exome Aggregation Consortium	Global	Study-wide	116280	A=0.200	T=0.799
The Exome Aggregation Consortium	Other	Sub	872	A=0.160	T=0.840
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.302	T=0.697
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.174	T=0.826

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
rs1654413	0.0000178	cocaine dependence	23958962
rs1654413	0.0000463	cocaine dependence	23958962

eQTL of rs1654413 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:55526359	GP6	ENSG00000088053.7	A>T	9.0091e-6	-23273	Cerebellum
Chr19:55526359	GP6	ENSG00000088053.7	A>T	1.2367e-4	-23273	Cerebellar_Hemisphere

meQTL of rs1654413 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	-49095
chr19	950706	950795	E067	-38564
chr19	983359	983479	E067	-5880
chr19	983553	983756	E067	-5603
chr19	1015608	1015844	E067	26249
chr19	1015851	1016391	E067	26492
chr19	1016489	1017758	E067	27130
chr19	1017787	1017841	E067	28428
chr19	1017842	1017926	E067	28483
chr19	1018058	1018350	E067	28699
chr19	1018426	1018691	E067	29067
chr19	1018760	1018893	E067	29401
chr19	941664	941993	E068	-47366
chr19	983359	983479	E068	-5880
chr19	983553	983756	E068	-5603
chr19	1015608	1015844	E068	26249
chr19	1015851	1016391	E068	26492
chr19	1016489	1017758	E068	27130
chr19	1017787	1017841	E068	28428
chr19	1017842	1017926	E068	28483
chr19	1018058	1018350	E068	28699
chr19	1018426	1018691	E068	29067
chr19	1018760	1018893	E068	29401
chr19	941664	941993	E069	-47366
chr19	983359	983479	E069	-5880
chr19	983553	983756	E069	-5603
chr19	995473	995566	E069	6114
chr19	1015851	1016391	E069	26492
chr19	1016489	1017758	E069	27130
chr19	1017787	1017841	E069	28428
chr19	1017842	1017926	E069	28483
chr19	1018058	1018350	E069	28699
chr19	1018426	1018691	E069	29067
chr19	1018760	1018893	E069	29401
chr19	940207	940264	E070	-49095
chr19	941664	941993	E070	-47366
chr19	942242	942572	E070	-46787
chr19	942585	942669	E070	-46690
chr19	944845	945548	E070	-43811
chr19	955812	957516	E070	-31843
chr19	983359	983479	E070	-5880
chr19	983553	983756	E070	-5603
chr19	985442	985779	E070	-3580
chr19	985854	986068	E070	-3291
chr19	1015608	1015844	E070	26249
chr19	1015851	1016391	E070	26492
chr19	1016489	1017758	E070	27130
chr19	1017787	1017841	E070	28428
chr19	1017842	1017926	E070	28483
chr19	1018058	1018350	E070	28699
chr19	1018426	1018691	E070	29067
chr19	1018760	1018893	E070	29401
chr19	940207	940264	E071	-49095
chr19	941664	941993	E071	-47366
chr19	983359	983479	E071	-5880
chr19	983553	983756	E071	-5603
chr19	1015608	1015844	E071	26249
chr19	1015851	1016391	E071	26492
chr19	1016489	1017758	E071	27130
chr19	1017787	1017841	E071	28428
chr19	1017842	1017926	E071	28483
chr19	1018058	1018350	E071	28699
chr19	1018426	1018691	E071	29067
chr19	1018760	1018893	E071	29401
chr19	941664	941993	E072	-47366
chr19	983359	983479	E072	-5880
chr19	983553	983756	E072	-5603
chr19	1015851	1016391	E072	26492
chr19	1016489	1017758	E072	27130
chr19	1017787	1017841	E072	28428
chr19	1017842	1017926	E072	28483
chr19	1018058	1018350	E072	28699
chr19	1018426	1018691	E072	29067
chr19	1018760	1018893	E072	29401
chr19	1015608	1015844	E073	26249
chr19	1015851	1016391	E073	26492
chr19	1016489	1017758	E073	27130
chr19	1017787	1017841	E073	28428
chr19	1017842	1017926	E073	28483
chr19	1018058	1018350	E073	28699
chr19	1018426	1018691	E073	29067
chr19	1018760	1018893	E073	29401
chr19	941664	941993	E074	-47366
chr19	983359	983479	E074	-5880
chr19	983553	983756	E074	-5603
chr19	1015851	1016391	E074	26492
chr19	1016489	1017758	E074	27130
chr19	1017787	1017841	E074	28428
chr19	1017842	1017926	E074	28483
chr19	1018058	1018350	E074	28699
chr19	1018426	1018691	E074	29067
chr19	1018760	1018893	E074	29401
chr19	940207	940264	E081	-49095
chr19	941664	941993	E081	-47366
chr19	983359	983479	E081	-5880
chr19	983553	983756	E081	-5603
chr19	985276	985326	E081	-4033
chr19	985442	985779	E081	-3580
chr19	1016489	1017758	E081	27130
chr19	1017787	1017841	E081	28428
chr19	1017842	1017926	E081	28483
chr19	1018058	1018350	E081	28699
chr19	1018426	1018691	E081	29067
chr19	1018760	1018893	E081	29401
chr19	940207	940264	E082	-49095
chr19	941664	941993	E082	-47366
chr19	944845	945548	E082	-43811
chr19	985276	985326	E082	-4033
chr19	985442	985779	E082	-3580
chr19	985854	986068	E082	-3291
chr19	986132	986303	E082	-3056
chr19	986710	986821	E082	-2538
chr19	1015851	1016391	E082	26492
chr19	1016489	1017758	E082	27130
chr19	1017787	1017841	E082	28428
chr19	1017842	1017926	E082	28483
chr19	1018058	1018350	E082	28699
chr19	1018426	1018691	E082	29067
chr19	1018760	1018893	E082	29401

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	983831	985184	E067	-4175
chr19	1019556	1022221	E067	30197
chr19	1025909	1029005	E067	36550
chr19	983831	985184	E068	-4175
chr19	1019556	1022221	E068	30197
chr19	1025909	1029005	E068	36550
chr19	983831	985184	E069	-4175
chr19	1019556	1022221	E069	30197
chr19	1025909	1029005	E069	36550
chr19	983831	985184	E070	-4175
chr19	1019556	1022221	E070	30197
chr19	983831	985184	E071	-4175
chr19	1019556	1022221	E071	30197
chr19	1025909	1029005	E071	36550
chr19	983831	985184	E072	-4175
chr19	1019556	1022221	E072	30197
chr19	1025909	1029005	E072	36550
chr19	983831	985184	E073	-4175
chr19	1019556	1022221	E073	30197
chr19	1025909	1029005	E073	36550
chr19	983831	985184	E074	-4175
chr19	1019556	1022221	E074	30197
chr19	1025909	1029005	E074	36550
chr19	1019556	1022221	E081	30197
chr19	983831	985184	E082	-4175
chr19	1000118	1000408	E082	10759
chr19	1019556	1022221	E082	30197
chr19	1025909	1029005	E082	36550