rs2119515

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0446 (13311/29826,GnomAD)
A=0449 (13092/29118,TOPMED)
A=0356 (1783/5008,1000G)
A=0495 (1908/3854,ALSPAC)
A=0487 (1805/3708,TWINSUK)

Position: chr2:129225558 (GRCh38.p7) (2q21.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 104 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.129225558G>A
GRCh38.p7 chr 2	NC_000002.12:g.129225558G>T
GRCh37.p13 chr 2	NC_000002.11:g.129983131G>A
GRCh37.p13 chr 2	NC_000002.11:g.129983131G>T

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.582	A=0.418
1000Genomes	American	Sub	694	G=0.680	A=0.320
1000Genomes	East Asian	Sub	1008	G=0.835	A=0.165
1000Genomes	Europe	Sub	1006	G=0.489	A=0.511
1000Genomes	Global	Study-wide	5008	G=0.644	A=0.356
1000Genomes	South Asian	Sub	978	G=0.670	A=0.330
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.505	A=0.495
The Genome Aggregation Database	African	Sub	8672	G=0.594	T=0.000
The Genome Aggregation Database	American	Sub	832	G=0.680	T=0.00,
The Genome Aggregation Database	East Asian	Sub	1618	G=0.863	T=0.000
The Genome Aggregation Database	Europe	Sub	18402	G=0.503	T=0.000
The Genome Aggregation Database	Global	Study-wide	29826	G=0.553	T=0.000
The Genome Aggregation Database	Other	Sub	302	G=0.410	T=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.550	A=0.449
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.513	A=0.487

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs2119515	9.42E-06	alcohol dependence (age at onset)	24962325

eQTL of rs2119515 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 rs2119515 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 )
chr2	72463657	72463893	E067	-29421
chr2	72463937	72464022	E067	-29292
chr2	72490258	72490489	E067	-2825
chr2	72490583	72490692	E067	-2622
chr2	72490890	72491183	E067	-2131
chr2	72498172	72498415	E067	4858
chr2	72498488	72498617	E067	5174
chr2	72498688	72498837	E067	5374
chr2	72498860	72499637	E067	5546
chr2	72450002	72450601	E068	-42713
chr2	72490258	72490489	E068	-2825
chr2	72490583	72490692	E068	-2622
chr2	72490890	72491183	E068	-2131
chr2	72498172	72498415	E068	4858
chr2	72498488	72498617	E068	5174
chr2	72498688	72498837	E068	5374
chr2	72498860	72499637	E068	5546
chr2	72499643	72499967	E068	6329
chr2	72501508	72501864	E068	8194
chr2	72501889	72502025	E068	8575
chr2	72502028	72502189	E068	8714
chr2	72450002	72450601	E069	-42713
chr2	72463657	72463893	E069	-29421
chr2	72463937	72464022	E069	-29292
chr2	72490258	72490489	E069	-2825
chr2	72490583	72490692	E069	-2622
chr2	72490890	72491183	E069	-2131
chr2	72498172	72498415	E069	4858
chr2	72498488	72498617	E069	5174
chr2	72498688	72498837	E069	5374
chr2	72498860	72499637	E069	5546
chr2	72501508	72501864	E069	8194
chr2	72501889	72502025	E069	8575
chr2	72502028	72502189	E069	8714
chr2	72502331	72502512	E069	9017
chr2	72502799	72503047	E069	9485
chr2	72507880	72508013	E069	14566
chr2	72540991	72541127	E069	47677
chr2	72541335	72541386	E069	48021
chr2	72485270	72485441	E070	-7873
chr2	72498488	72498617	E070	5174
chr2	72498688	72498837	E070	5374
chr2	72498860	72499637	E070	5546
chr2	72501889	72502025	E070	8575
chr2	72502028	72502189	E070	8714
chr2	72502331	72502512	E070	9017
chr2	72502799	72503047	E070	9485
chr2	72503092	72503142	E070	9778
chr2	72503195	72503325	E070	9881
chr2	72450002	72450601	E071	-42713
chr2	72463265	72463344	E071	-29970
chr2	72463657	72463893	E071	-29421
chr2	72463937	72464022	E071	-29292
chr2	72490258	72490489	E071	-2825
chr2	72490583	72490692	E071	-2622
chr2	72490890	72491183	E071	-2131
chr2	72498172	72498415	E071	4858
chr2	72498488	72498617	E071	5174
chr2	72498688	72498837	E071	5374
chr2	72498860	72499637	E071	5546
chr2	72499643	72499967	E071	6329
chr2	72501508	72501864	E071	8194
chr2	72501889	72502025	E071	8575
chr2	72502028	72502189	E071	8714
chr2	72502331	72502512	E071	9017
chr2	72502799	72503047	E071	9485
chr2	72503092	72503142	E071	9778
chr2	72503195	72503325	E071	9881
chr2	72503481	72503531	E071	10167
chr2	72450002	72450601	E072	-42713
chr2	72490258	72490489	E072	-2825
chr2	72490583	72490692	E072	-2622
chr2	72490890	72491183	E072	-2131
chr2	72498860	72499637	E072	5546
chr2	72499643	72499967	E072	6329
chr2	72502028	72502189	E072	8714
chr2	72490890	72491183	E073	-2131
chr2	72498488	72498617	E073	5174
chr2	72498688	72498837	E073	5374
chr2	72498860	72499637	E073	5546
chr2	72502331	72502512	E073	9017
chr2	72450002	72450601	E074	-42713
chr2	72490258	72490489	E074	-2825
chr2	72490583	72490692	E074	-2622
chr2	72490890	72491183	E074	-2131
chr2	72498488	72498617	E074	5174
chr2	72498688	72498837	E074	5374
chr2	72498860	72499637	E074	5546
chr2	72499643	72499967	E074	6329
chr2	72500741	72500888	E074	7427
chr2	72501272	72501389	E074	7958
chr2	72501508	72501864	E074	8194
chr2	72501889	72502025	E074	8575
chr2	72502028	72502189	E074	8714
chr2	72502331	72502512	E074	9017
chr2	72502799	72503047	E074	9485
chr2	72503092	72503142	E074	9778
chr2	72503195	72503325	E074	9881
chr2	72503481	72503531	E074	10167
chr2	72498860	72499637	E081	5546
chr2	72499643	72499967	E081	6329
chr2	72501889	72502025	E081	8575
chr2	72502028	72502189	E081	8714
chr2	72502331	72502512	E081	9017