rs3131513

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0331 (9899/29900,GnomAD)
G==0295 (8615/29118,TOPMED)
G==0290 (1454/5008,1000G)
G==0391 (1508/3854,ALSPAC)
G==0385 (1429/3708,TWINSUK)

Position: chr1:24866664 (GRCh38.p7) (1p36.11)

Phenotype: AD | ND

Dataset:

GWASdb2 | GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 118 Enhancers around

Promoter: 8 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.24866664G>A
GRCh37.p13 chr 1	NC_000001.10:g.25193155G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.138	A=0.862
1000Genomes	American	Sub	694	G=0.460	A=0.540
1000Genomes	East Asian	Sub	1008	G=0.296	A=0.704
1000Genomes	Europe	Sub	1006	G=0.402	A=0.598
1000Genomes	Global	Study-wide	5008	G=0.290	A=0.710
1000Genomes	South Asian	Sub	978	G=0.260	A=0.740
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.391	A=0.609
The Genome Aggregation Database	African	Sub	8714	G=0.177	A=0.823
The Genome Aggregation Database	American	Sub	836	G=0.420	A=0.580
The Genome Aggregation Database	East Asian	Sub	1612	G=0.282	A=0.718
The Genome Aggregation Database	Europe	Sub	18436	G=0.404	A=0.595
The Genome Aggregation Database	Global	Study-wide	29900	G=0.331	A=0.668
The Genome Aggregation Database	Other	Sub	302	G=0.260	A=0.740
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.295	A=0.704
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.385	A=0.615

PMID	Title	Author	Journal
23942779	A genome-wide association study of behavioral disinhibition.	McGue M	Behav Genet

P-Value

SNP ID	p-value	Traits	Study
rs3131513	0.000002	alcohol dependence	23942779
rs3131513	0.00032	nicotine use	23942779

eQTL of rs3131513 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs3131513 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 )
chr1	25149497	25149649	E067	-43506
chr1	25152841	25153064	E067	-40091
chr1	25153101	25153283	E067	-39872
chr1	25154083	25154278	E067	-38877
chr1	25154340	25154555	E067	-38600
chr1	25154705	25155234	E067	-37921
chr1	25155268	25155319	E067	-37836
chr1	25155375	25155521	E067	-37634
chr1	25156274	25156324	E067	-36831
chr1	25156745	25156795	E067	-36360
chr1	25157098	25157628	E067	-35527
chr1	25175474	25175600	E067	-17555
chr1	25219911	25219954	E067	26756
chr1	25239980	25240118	E067	46825
chr1	25240466	25240563	E067	47311
chr1	25240611	25241651	E067	47456
chr1	25149497	25149649	E068	-43506
chr1	25152841	25153064	E068	-40091
chr1	25153101	25153283	E068	-39872
chr1	25154083	25154278	E068	-38877
chr1	25154340	25154555	E068	-38600
chr1	25154705	25155234	E068	-37921
chr1	25155268	25155319	E068	-37836
chr1	25155375	25155521	E068	-37634
chr1	25156274	25156324	E068	-36831
chr1	25156745	25156795	E068	-36360
chr1	25157098	25157628	E068	-35527
chr1	25157720	25157770	E068	-35385
chr1	25240611	25241651	E068	47456
chr1	25148088	25148138	E069	-45017
chr1	25149497	25149649	E069	-43506
chr1	25149860	25149900	E069	-43255
chr1	25152841	25153064	E069	-40091
chr1	25153101	25153283	E069	-39872
chr1	25154083	25154278	E069	-38877
chr1	25154340	25154555	E069	-38600
chr1	25154705	25155234	E069	-37921
chr1	25155268	25155319	E069	-37836
chr1	25155375	25155521	E069	-37634
chr1	25156274	25156324	E069	-36831
chr1	25156745	25156795	E069	-36360
chr1	25157098	25157628	E069	-35527
chr1	25157720	25157770	E069	-35385
chr1	25158098	25158148	E069	-35007
chr1	25158340	25158556	E069	-34599
chr1	25158585	25158668	E069	-34487
chr1	25219545	25219637	E069	26390
chr1	25219711	25219878	E069	26556
chr1	25219911	25219954	E069	26756
chr1	25220117	25220244	E069	26962
chr1	25220696	25220833	E069	27541
chr1	25240466	25240563	E069	47311
chr1	25240611	25241651	E069	47456
chr1	25152841	25153064	E070	-40091
chr1	25153101	25153283	E070	-39872
chr1	25175474	25175600	E070	-17555
chr1	25149497	25149649	E071	-43506
chr1	25149860	25149900	E071	-43255
chr1	25152841	25153064	E071	-40091
chr1	25153101	25153283	E071	-39872
chr1	25154083	25154278	E071	-38877
chr1	25154340	25154555	E071	-38600
chr1	25154705	25155234	E071	-37921
chr1	25155268	25155319	E071	-37836
chr1	25155375	25155521	E071	-37634
chr1	25156274	25156324	E071	-36831
chr1	25156745	25156795	E071	-36360
chr1	25157098	25157628	E071	-35527
chr1	25157720	25157770	E071	-35385
chr1	25158098	25158148	E071	-35007
chr1	25158340	25158556	E071	-34599
chr1	25158585	25158668	E071	-34487
chr1	25165272	25165352	E071	-27803
chr1	25175474	25175600	E071	-17555
chr1	25175638	25175788	E071	-17367
chr1	25175881	25175982	E071	-17173
chr1	25176121	25176636	E071	-16519
chr1	25219711	25219878	E071	26556
chr1	25219911	25219954	E071	26756
chr1	25220117	25220244	E071	26962
chr1	25220696	25220833	E071	27541
chr1	25240466	25240563	E071	47311
chr1	25240611	25241651	E071	47456
chr1	25149497	25149649	E072	-43506
chr1	25152841	25153064	E072	-40091
chr1	25153101	25153283	E072	-39872
chr1	25219711	25219878	E072	26556
chr1	25219911	25219954	E072	26756
chr1	25220117	25220244	E072	26962
chr1	25240611	25241651	E072	47456
chr1	25152841	25153064	E073	-40091
chr1	25153101	25153283	E073	-39872
chr1	25240466	25240563	E073	47311
chr1	25149497	25149649	E074	-43506
chr1	25152841	25153064	E074	-40091
chr1	25153101	25153283	E074	-39872
chr1	25154083	25154278	E074	-38877
chr1	25154340	25154555	E074	-38600
chr1	25154705	25155234	E074	-37921
chr1	25155268	25155319	E074	-37836
chr1	25155375	25155521	E074	-37634
chr1	25156274	25156324	E074	-36831
chr1	25156745	25156795	E074	-36360
chr1	25157098	25157628	E074	-35527
chr1	25157720	25157770	E074	-35385
chr1	25158098	25158148	E074	-35007
chr1	25158340	25158556	E074	-34599
chr1	25158585	25158668	E074	-34487
chr1	25219490	25219540	E074	26335
chr1	25219545	25219637	E074	26390
chr1	25219711	25219878	E074	26556
chr1	25219911	25219954	E074	26756
chr1	25220117	25220244	E074	26962
chr1	25220696	25220833	E074	27541
chr1	25240466	25240563	E074	47311
chr1	25175474	25175600	E081	-17555
chr1	25175638	25175788	E081	-17367
chr1	25175881	25175982	E081	-17173

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	25174304	25175421	E067	-17734
chr1	25174304	25175421	E068	-17734
chr1	25174304	25175421	E069	-17734
chr1	25174304	25175421	E071	-17734
chr1	25174304	25175421	E072	-17734
chr1	25174304	25175421	E073	-17734
chr1	25174304	25175421	E074	-17734
chr1	25174304	25175421	E082	-17734