rs2961557

Organism: Homo sapiens

Alleles: A>C / A>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0124 (3729/29976,GnomAD)
A==0129 (3776/29118,TOPMED)
A==0118 (590/5008,1000G)
A==0136 (523/3854,ALSPAC)
A==0131 (484/3708,TWINSUK)

Position: chr12:11956571 (GRCh38.p7) (12p13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 53 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.11956571A>C
GRCh38.p7 chr 12	NC_000012.12:g.11956571A>T
GRCh37.p13 chr 12	NC_000012.11:g.12109505A>C
GRCh37.p13 chr 12	NC_000012.11:g.12109505A>T

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.138	C=0.862
1000Genomes	American	Sub	694	A=0.150	C=0.850
1000Genomes	East Asian	Sub	1008	A=0.070	C=0.930
1000Genomes	Europe	Sub	1006	A=0.124	C=0.876
1000Genomes	Global	Study-wide	5008	A=0.118	C=0.882
1000Genomes	South Asian	Sub	978	A=0.110	C=0.890
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.136	C=0.864
The Genome Aggregation Database	African	Sub	8716	A=0.136	C=0.864
The Genome Aggregation Database	American	Sub	838	A=0.150	C=0.850
The Genome Aggregation Database	East Asian	Sub	1622	A=0.061	C=0.939
The Genome Aggregation Database	Europe	Sub	18500	A=0.124	C=0.875
The Genome Aggregation Database	Global	Study-wide	29976	A=0.124	C=0.875
The Genome Aggregation Database	Other	Sub	300	A=0.040	C=0.960
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.129	C=0.870
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.131	C=0.869

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs2961557	0.00087	alcohol dependence	20201924

eQTL of rs2961557 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 rs2961557 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 )
chr12	42313298	42313731	E067	47929
chr12	42314045	42314547	E067	48676
chr12	42314597	42314683	E067	49228
chr12	42314745	42314845	E068	49376
chr12	42263335	42263502	E070	-1867
chr12	42298374	42298424	E070	33005
chr12	42298476	42298533	E070	33107
chr12	42298609	42298659	E070	33240
chr12	42298882	42299266	E070	33513
chr12	42304442	42304667	E070	39073
chr12	42304756	42304988	E070	39387
chr12	42305063	42305157	E070	39694
chr12	42305221	42305271	E070	39852
chr12	42305601	42305651	E070	40232
chr12	42305825	42305877	E070	40456
chr12	42309969	42310197	E070	44600
chr12	42310842	42310892	E070	45473
chr12	42311534	42311608	E070	46165
chr12	42311727	42312349	E070	46358
chr12	42312634	42312687	E070	47265
chr12	42312703	42312792	E070	47334
chr12	42312935	42312989	E070	47566
chr12	42314745	42314845	E070	49376
chr12	42314920	42314970	E070	49551
chr12	42315179	42315229	E070	49810
chr12	42314045	42314547	E071	48676
chr12	42314597	42314683	E071	49228
chr12	42276104	42276277	E074	10735
chr12	42298374	42298424	E081	33005
chr12	42304442	42304667	E081	39073
chr12	42304756	42304988	E081	39387
chr12	42305063	42305157	E081	39694
chr12	42305221	42305271	E081	39852
chr12	42311534	42311608	E081	46165
chr12	42311727	42312349	E081	46358
chr12	42312634	42312687	E081	47265
chr12	42312703	42312792	E081	47334
chr12	42312935	42312989	E081	47566
chr12	42313298	42313731	E081	47929
chr12	42314045	42314547	E081	48676
chr12	42314597	42314683	E081	49228
chr12	42298374	42298424	E082	33005
chr12	42298476	42298533	E082	33107
chr12	42298609	42298659	E082	33240
chr12	42298882	42299266	E082	33513
chr12	42300863	42301530	E082	35494
chr12	42304442	42304667	E082	39073
chr12	42304756	42304988	E082	39387
chr12	42305063	42305157	E082	39694
chr12	42305221	42305271	E082	39852
chr12	42313298	42313731	E082	47929
chr12	42314045	42314547	E082	48676
chr12	42314597	42314683	E082	49228

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	42313773	42314036	E067	48404
chr12	42313773	42314036	E068	48404
chr12	42313773	42314036	E069	48404
chr12	42313773	42314036	E070	48404
chr12	42313773	42314036	E071	48404
chr12	42313773	42314036	E072	48404
chr12	42313773	42314036	E073	48404
chr12	42313773	42314036	E074	48404
chr12	42313773	42314036	E082	48404