SNP Detail Info-rs12142820

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0430 (12844/29806,GnomAD)
T=0373 (1870/5008,1000G)
T=0494 (1905/3854,ALSPAC)
T=0493 (1827/3708,TWINSUK)

Position: chr1:59250371 (GRCh38.p7) (1p32.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 14 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.59250371A>T
GRCh37.p13 chr 1	NC_000001.10:g.59716043A>T

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.681	T=0.319
1000Genomes	American	Sub	694	A=0.590	T=0.410
1000Genomes	East Asian	Sub	1008	A=0.645	T=0.355
1000Genomes	Europe	Sub	1006	A=0.525	T=0.475
1000Genomes	Global	Study-wide	5008	A=0.627	T=0.373
1000Genomes	South Asian	Sub	978	A=0.660	T=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.506	T=0.494
The Genome Aggregation Database	African	Sub	8676	A=0.667	T=0.333
The Genome Aggregation Database	American	Sub	830	A=0.570	T=0.430
The Genome Aggregation Database	East Asian	Sub	1598	A=0.642	T=0.358
The Genome Aggregation Database	Europe	Sub	18400	A=0.516	T=0.483
The Genome Aggregation Database	Global	Study-wide	29806	A=0.569	T=0.430
The Genome Aggregation Database	Other	Sub	302	A=0.580	T=0.420
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.507	T=0.493

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs12142820	0.00051	alcohol dependence	21314694

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

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	59714840	59714982	E068	-1061
chr1	59716153	59716227	E068	110
chr1	59716429	59716521	E068	386
chr1	59764287	59764377	E068	48244
chr1	59764449	59764864	E068	48406
chr1	59763481	59764259	E069	47438
chr1	59764287	59764377	E069	48244
chr1	59764449	59764864	E069	48406
chr1	59764958	59765029	E069	48915
chr1	59760801	59760865	E071	44758
chr1	59761041	59761105	E071	44998
chr1	59763481	59764259	E071	47438
chr1	59761041	59761105	E072	44998
chr1	59763481	59764259	E072	47438

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	59761186	59763209	E067	45143
chr1	59761186	59763209	E068	45143
chr1	59761186	59763209	E069	45143
chr1	59761186	59763209	E070	45143
chr1	59761186	59763209	E071	45143
chr1	59761186	59763209	E072	45143
chr1	59761186	59763209	E073	45143
chr1	59761186	59763209	E074	45143
chr1	59761186	59763209	E081	45143
chr1	59761186	59763209	E082	45143

rs12142820