rs16945949

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0074 (2223/29964,GnomAD)
A=0113 (3305/29118,TOPMED)
A=0078 (391/5008,1000G)
A=0001 (5/3854,ALSPAC)
A=0001 (2/3708,TWINSUK)

Position: chr15:62853703 (GRCh38.p7) (15q22.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 75 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.62853703G>A
GRCh37.p13 chr 15	NC_000015.9:g.63145902G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.713	A=0.287
1000Genomes	American	Sub	694	G=0.990	A=0.010
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=0.998	A=0.002
1000Genomes	Global	Study-wide	5008	G=0.922	A=0.078
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.999	A=0.001
The Genome Aggregation Database	African	Sub	8712	G=0.748	A=0.252
The Genome Aggregation Database	American	Sub	838	G=0.990	A=0.010
The Genome Aggregation Database	East Asian	Sub	1622	G=1.000	A=0.000
The Genome Aggregation Database	Europe	Sub	18490	G=0.999	A=0.000
The Genome Aggregation Database	Global	Study-wide	29964	G=0.925	A=0.074
The Genome Aggregation Database	Other	Sub	302	G=1.000	A=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.886	A=0.113
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.999	A=0.001

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
rs16945949	0.000512	alcohol dependence	20201924

eQTL of rs16945949 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 rs16945949 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 )
chr15	63117338	63117746	E067	-28156
chr15	63120086	63120136	E067	-25766
chr15	63120146	63120186	E067	-25716
chr15	63120268	63120329	E067	-25573
chr15	63120437	63121018	E067	-24884
chr15	63139795	63140416	E067	-5486
chr15	63140609	63140744	E067	-5158
chr15	63140755	63141160	E067	-4742
chr15	63145022	63145077	E067	-825
chr15	63145129	63145269	E067	-633
chr15	63145656	63146083	E067	0
chr15	63146127	63146430	E067	225
chr15	63146453	63146577	E067	551
chr15	63146695	63146745	E067	793
chr15	63146795	63146997	E067	893
chr15	63145022	63145077	E068	-825
chr15	63145129	63145269	E068	-633
chr15	63117150	63117300	E069	-28602
chr15	63117338	63117746	E069	-28156
chr15	63120437	63121018	E069	-24884
chr15	63145022	63145077	E069	-825
chr15	63145129	63145269	E069	-633
chr15	63145446	63145496	E069	-406
chr15	63145656	63146083	E069	0
chr15	63146127	63146430	E069	225
chr15	63146453	63146577	E069	551
chr15	63178660	63179587	E070	32758
chr15	63117150	63117300	E071	-28602
chr15	63117338	63117746	E071	-28156
chr15	63120268	63120329	E071	-25573
chr15	63140609	63140744	E071	-5158
chr15	63140755	63141160	E071	-4742
chr15	63141166	63141276	E071	-4626
chr15	63145022	63145077	E071	-825
chr15	63145129	63145269	E071	-633
chr15	63145446	63145496	E071	-406
chr15	63145656	63146083	E071	0
chr15	63146127	63146430	E071	225
chr15	63146453	63146577	E071	551
chr15	63146695	63146745	E071	793
chr15	63146795	63146997	E071	893
chr15	63179632	63179894	E071	33730
chr15	63120437	63121018	E072	-24884
chr15	63121095	63121274	E072	-24628
chr15	63139795	63140416	E072	-5486
chr15	63140609	63140744	E072	-5158
chr15	63140755	63141160	E072	-4742
chr15	63145022	63145077	E072	-825
chr15	63145129	63145269	E072	-633
chr15	63145446	63145496	E072	-406
chr15	63145656	63146083	E072	0
chr15	63146127	63146430	E072	225
chr15	63146453	63146577	E072	551
chr15	63120437	63121018	E073	-24884
chr15	63145022	63145077	E073	-825
chr15	63145129	63145269	E073	-633
chr15	63145446	63145496	E073	-406
chr15	63145656	63146083	E073	0
chr15	63146127	63146430	E073	225
chr15	63117150	63117300	E074	-28602
chr15	63117338	63117746	E074	-28156
chr15	63140609	63140744	E074	-5158
chr15	63145022	63145077	E074	-825
chr15	63145129	63145269	E074	-633
chr15	63145446	63145496	E074	-406
chr15	63145656	63146083	E074	0
chr15	63146127	63146430	E074	225
chr15	63179632	63179894	E074	33730
chr15	63173285	63173359	E081	27383
chr15	63173445	63173555	E081	27543
chr15	63173581	63173674	E081	27679
chr15	63189993	63190236	E081	44091
chr15	63190276	63190564	E081	44374
chr15	63190570	63190631	E081	44668
chr15	63179632	63179894	E082	33730