rs904092

Organism: Homo sapiens

Alleles: A>G / A>T

Gene : Feature

ADH1A : 2KB Upstream Variant
LOC100507053 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0184 (5520/29956,GnomAD)
A==0200 (5829/29118,TOPMED)
A==0171 (854/5008,1000G)

Position: chr4:99293007 (GRCh38.p7) (4q23)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 5 publication(s)

Genomic View: See rs on genome

Enhancer: 6 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.99293007A>G
GRCh38.p7 chr 4	NC_000004.12:g.99293007A>T
GRCh37.p13 chr 4	NC_000004.11:g.100214164A>G
GRCh37.p13 chr 4	NC_000004.11:g.100214164A>T

Gene: ADH1A, alcohol dehydrogenase 1A (class I), alpha polypeptide(minus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ADH1A transcript	NM_000667.3:c.	N/A	Upstream Transcript Variant
ADH1A transcript variant X1	XR_001741125.1:n.	N/A	N/A

Gene: LOC100507053, uncharacterized LOC100507053(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.203	G=0.797
1000Genomes	American	Sub	694	A=0.180	G=0.820
1000Genomes	East Asian	Sub	1008	A=0.089	G=0.911
1000Genomes	Europe	Sub	1006	A=0.145	G=0.855
1000Genomes	Global	Study-wide	5008	A=0.171	G=0.829
1000Genomes	South Asian	Sub	978	A=0.230	G=0.770
The Genome Aggregation Database	African	Sub	8718	A=0.230	G=0.770
The Genome Aggregation Database	American	Sub	834	A=0.200	G=0.80,
The Genome Aggregation Database	East Asian	Sub	1620	A=0.089	G=0.911
The Genome Aggregation Database	Europe	Sub	18482	A=0.171	G=0.829
The Genome Aggregation Database	Global	Study-wide	29956	A=0.184	G=0.815
The Genome Aggregation Database	Other	Sub	302	A=0.150	G=0.85,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.200	G=0.799

PMID	Title	Author	Journal
24166409	Genome-wide association study of alcohol dependence:significant findings in African- and European-Americans including novel risk loci.	Gelernter J	Mol Psychiatry
19193628	ADH single nucleotide polymorphism associations with alcohol metabolism in vivo.	Birley AJ	Hum Mol Genet
18331377	Association of ADH and ALDH genes with alcohol dependence in the Irish Affected Sib Pair Study of alcohol dependence (IASPSAD) sample.	Kuo PH	Alcohol Clin Exp Res
21083667	Haplotype-based study of the association of alcohol-metabolizing genes with alcohol dependence in four independent populations.	Liu J	Alcohol Clin Exp Res
19526455	ADH1A variation predisposes to personality traits and substance dependence.	Zuo L	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs904092	5.00E-09	alcohol dependence(AA)	24166409
rs904092	9.00E-06	alcohol dependence(ALL)	24166409

eQTL of rs904092 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 rs904092 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 )
chr4	100245602	100245886	E068	8840
chr4	100221669	100221897	E070	-14865
chr4	100244954	100245162	E073	8192
chr4	100245344	100245493	E073	8582
chr4	100221669	100221897	E082	-14865
chr4	100222048	100222444	E082	-14318