rs1789924

Homo sapiens
C>T
ADH1C : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0334 (9995/29916,GnomAD)
T=0262 (7629/29118,TOPMED)
T=0216 (1083/5008,1000G)
T=0399 (1538/3854,ALSPAC)
T=0411 (1523/3708,TWINSUK)
chr4:99353129 (GRCh38.p7) (4q23)
AD
GWASCatalog
14   publication(s)
See rs on genome
3 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.99353129C>T
GRCh37.p13 chr 4NC_000004.11:g.100274286C>T
ADH1C RefSeqGeneNG_011718.1:g.4632G>A

Gene: ADH1C, alcohol dehydrogenase 1C (class I), gamma polypeptide(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
ADH1C transcript variant 1NM_000669.4:c.N/AUpstream Transcript Variant
ADH1C transcript variant 2NR_133005.1:n.N/AUpstream Transcript Variant
ADH1C transcript variant X1XM_011531588.2:c.N/AUpstream Transcript Variant
ADH1C transcript variant X2XM_011531589.1:c.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.900T=0.100
1000GenomesAmericanSub694C=0.730T=0.270
1000GenomesEast AsianSub1008C=0.923T=0.077
1000GenomesEuropeSub1006C=0.595T=0.405
1000GenomesGlobalStudy-wide5008C=0.784T=0.216
1000GenomesSouth AsianSub978C=0.720T=0.280
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.601T=0.399
The Genome Aggregation DatabaseAfricanSub8710C=0.854T=0.146
The Genome Aggregation DatabaseAmericanSub838C=0.680T=0.320
The Genome Aggregation DatabaseEast AsianSub1618C=0.913T=0.087
The Genome Aggregation DatabaseEuropeSub18448C=0.553T=0.446
The Genome Aggregation DatabaseGlobalStudy-wide29916C=0.665T=0.334
The Genome Aggregation DatabaseOtherSub302C=0.750T=0.250
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.738T=0.262
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.589T=0.411
PMID Title Author Journal
24166409Genome-wide association study of alcohol dependence:significant findings in African- and European-Americans including novel risk loci.Gelernter JMol Psychiatry
19298322Associations and interactions between SNPs in the alcohol metabolizing genes and alcoholism phenotypes in European Americans.Sherva RAlcohol Clin Exp Res
26396927Impact of multiple Alcohol Dehydrogenase gene polymorphisms on risk of laryngeal, esophageal, gastric and colorectal cancers in Chinese Han population.An JAm J Cancer Res
21635275Association of alcohol dehydrogenase genes with alcohol-related phenotypes in a Native American community sample.Gizer IRAlcohol Clin Exp Res
25133033Epidemiological studies of esophageal cancer in the era of genome-wide association studies.Wang AHWorld J Gastrointest Pathophysiol
23430454Genetic variants at 4q21, 4q23 and 12q24 are associated with esophageal squamous cell carcinoma risk in a Chinese population.Gao YHum Genet
28714907Genetic Contribution to Alcohol Dependence: Investigation of a Heterogeneous German Sample of Individuals with Alcohol Dependence, Chronic Alcoholic Pancreatitis, and Alcohol-Related Cirrhosis.Treutlein JGenes (Basel)
22004471Genome-wide significant association between alcohol dependence and a variant in the ADH gene cluster.Frank JAddict Biol
21819567Case-control study for colorectal cancer genetic susceptibility in EPICOLON: previously identified variants and mucins.Abuli ABMC Cancer
22662130Using prior information from the medical literature in GWAS of oral cancer identifies novel susceptibility variant on chromosome 4--the AdAPT method.Johansson MPLoS One
17273965Evidence of positive selection on a class I ADH locus.Han YAm J Hum Genet
21437268A genome-wide association study of upper aerodigestive tract cancers conducted within the INHANCE consortium.McKay JDPLoS Genet
19193628ADH single nucleotide polymorphism associations with alcohol metabolism in vivo.Birley AJHum Mol Genet
22674868Genetic variants at 4q23 and 12q24 are associated with head and neck cancer risk in China.Yuan HMol Carcinog

P-Value

SNP ID p-value Traits Study
rs17899241.00E-07alcohol dependence28714907
rs17899246.00E-06alcohol dependence24166409

eQTL of rs1789924 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 rs1789924 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 )
chr4100245602100245886E068-28400
chr4100244954100245162E073-29124
chr4100245344100245493E073-28793