rs3791853

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

GAD1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0051 (1538/29968,GnomAD)
G=0051 (1506/29118,TOPMED)
G=0103 (517/5008,1000G)
G=0031 (120/3854,ALSPAC)
G=0023 (87/3708,TWINSUK)

Position: chr2:170838560 (GRCh38.p7) (2q31.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 14 Enhancers around

Promoter: 42 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
GAD1 transcript variant GAD67	NM_000817.2:c.	N/A	Intron Variant
GAD1 transcript variant GAD25	NM_013445.3:c.	N/A	Intron Variant
GAD1 transcript variant X5	XM_005246444.2:c.	N/A	Intron Variant
GAD1 transcript variant X2	XM_011510922.1:c.	N/A	Intron Variant
GAD1 transcript variant X1	XM_017003756.1:c.	N/A	Intron Variant
GAD1 transcript variant X3	XM_017003757.1:c.	N/A	Intron Variant
GAD1 transcript variant X4	XM_017003758.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.943	G=0.057
1000Genomes	American	Sub	694	A=0.850	G=0.150
1000Genomes	East Asian	Sub	1008	A=0.726	G=0.274
1000Genomes	Europe	Sub	1006	A=0.986	G=0.014
1000Genomes	Global	Study-wide	5008	A=0.897	G=0.103
1000Genomes	South Asian	Sub	978	A=0.950	G=0.050
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.969	G=0.031
The Genome Aggregation Database	African	Sub	8728	A=0.937	G=0.063
The Genome Aggregation Database	American	Sub	838	A=0.840	G=0.160
The Genome Aggregation Database	East Asian	Sub	1602	A=0.748	G=0.252
The Genome Aggregation Database	Europe	Sub	18498	A=0.975	G=0.024
The Genome Aggregation Database	Global	Study-wide	29968	A=0.948	G=0.051
The Genome Aggregation Database	Other	Sub	302	A=0.990	G=0.010
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.948	G=0.051
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.977	G=0.023

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
rs3791853	0.000293	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

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	171729398	171729483	E067	34328
chr2	171729398	171729483	E068	34328
chr2	171682251	171682301	E070	-12769
chr2	171683074	171683323	E070	-11747
chr2	171683344	171683398	E070	-11672
chr2	171729398	171729483	E070	34328
chr2	171737343	171737504	E070	42273
chr2	171729398	171729483	E071	34328
chr2	171729515	171730249	E071	34445
chr2	171729398	171729483	E072	34328
chr2	171729515	171730249	E072	34445
chr2	171729398	171729483	E074	34328
chr2	171683691	171683741	E081	-11329
chr2	171683344	171683398	E082	-11672

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	171672030	171673064	E067	-22006
chr2	171673083	171673718	E067	-21352
chr2	171673770	171674683	E067	-20387
chr2	171674798	171675766	E067	-19304
chr2	171678391	171678553	E067	-16517
chr2	171678842	171680098	E067	-14972
chr2	171673083	171673718	E068	-21352
chr2	171673770	171674683	E068	-20387
chr2	171674798	171675766	E068	-19304
chr2	171680197	171680615	E068	-14455
chr2	171673083	171673718	E069	-21352
chr2	171674798	171675766	E069	-19304
chr2	171680197	171680615	E069	-14455
chr2	171672030	171673064	E070	-22006
chr2	171673083	171673718	E070	-21352
chr2	171673770	171674683	E070	-20387
chr2	171674798	171675766	E070	-19304
chr2	171680197	171680615	E070	-14455
chr2	171680197	171680615	E071	-14455
chr2	171673083	171673718	E072	-21352
chr2	171673770	171674683	E072	-20387
chr2	171674798	171675766	E072	-19304
chr2	171677187	171678055	E072	-17015
chr2	171678842	171680098	E072	-14972
chr2	171680197	171680615	E072	-14455
chr2	171672030	171673064	E073	-22006
chr2	171673083	171673718	E073	-21352
chr2	171673770	171674683	E073	-20387
chr2	171674798	171675766	E073	-19304
chr2	171677187	171678055	E073	-17015
chr2	171678842	171680098	E073	-14972
chr2	171673083	171673718	E074	-21352
chr2	171673770	171674683	E074	-20387
chr2	171677187	171678055	E074	-17015
chr2	171678842	171680098	E074	-14972
chr2	171672030	171673064	E082	-22006
chr2	171673083	171673718	E082	-21352
chr2	171674798	171675766	E082	-19304
chr2	171677187	171678055	E082	-17015
chr2	171678391	171678553	E082	-16517
chr2	171678556	171678713	E082	-16357
chr2	171680197	171680615	E082	-14455