rs2298753

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

ADH1C : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0098 (11921/121088,ExAC)
C=0086 (2591/29968,GnomAD)
C=0062 (1829/29118,TOPMED)
T==0071 (929/13006,GO-ESP)
C=0064 (322/5008,1000G)
C=0087 (337/3854,ALSPAC)
C=0090 (335/3708,TWINSUK)

Position: chr4:99336750 (GRCh38.p7) (4q23)

Phenotype: AD

Dataset:

GWASdb2

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.99336750T>C
GRCh37.p13 chr 4	NC_000004.11:g.100257907T>C
ADH1C RefSeqGene	NG_011718.1:g.21011A>G

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

Molecule type	Change	Amino acid[Codon]	SO Term
ADH1C transcript variant 1	NM_000669.4:c.	N/A	3 Prime UTR Variant
ADH1C transcript variant 2	NR_133005.1:n.145...NR_133005.1:n.1456A>G	A>G	Non Coding Transcript Variant
ADH1C transcript variant X2	XM_011531589.1:c.	N/A	3 Prime UTR Variant
ADH1C transcript variant X1	XM_011531588.2:c.	N/A	3 Prime UTR Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.993	C=0.007
1000Genomes	American	Sub	694	T=0.900	C=0.100
1000Genomes	East Asian	Sub	1008	T=0.948	C=0.052
1000Genomes	Europe	Sub	1006	T=0.911	C=0.089
1000Genomes	Global	Study-wide	5008	T=0.936	C=0.064
1000Genomes	South Asian	Sub	978	T=0.900	C=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.913	C=0.087
The Exome Aggregation Consortium	American	Sub	21840	T=0.903	C=0.097
The Exome Aggregation Consortium	Asian	Sub	25126	T=0.911	C=0.088
The Exome Aggregation Consortium	Europe	Sub	73220	T=0.897	C=0.102
The Exome Aggregation Consortium	Global	Study-wide	121088	T=0.901	C=0.098
The Exome Aggregation Consortium	Other	Sub	902	T=0.880	C=0.120
The Genome Aggregation Database	African	Sub	8732	T=0.972	C=0.028
The Genome Aggregation Database	American	Sub	838	T=0.890	C=0.110
The Genome Aggregation Database	East Asian	Sub	1612	T=0.938	C=0.062
The Genome Aggregation Database	Europe	Sub	18484	T=0.884	C=0.115
The Genome Aggregation Database	Global	Study-wide	29968	T=0.913	C=0.086
The Genome Aggregation Database	Other	Sub	302	T=0.950	C=0.050
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.937	C=0.062
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.910	C=0.090

PMID	Title	Author	Journal
19193628	ADH single nucleotide polymorphism associations with alcohol metabolism in vivo.	Birley AJ	Hum Mol Genet
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res
20089146	The ADH1B Arg47His polymorphism in east Asian populations and expansion of rice domestication in history.	Peng Y	BMC Evol Biol
19298322	Associations and interactions between SNPs in the alcohol metabolizing genes and alcoholism phenotypes in European Americans.	Sherva R	Alcohol Clin Exp Res
21940907	Joint effects of alcohol consumption and polymorphisms in alcohol and oxidative stress metabolism genes on risk of head and neck cancer.	Hakenewerth AM	Cancer Epidemiol Biomarkers Prev

SNP ID	p-value	Traits	Study
rs2298753	0.000811	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr4:100257907	ADH1C	ENSG00000248144.1	T>C	3.8914e-4	-16277	Brain_Spinal_cord_cervical

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	-12021
chr4	100221669	100221897	E070	-36010
chr4	100244954	100245162	E073	-12745
chr4	100245344	100245493	E073	-12414
chr4	100221669	100221897	E082	-36010
chr4	100222048	100222444	E082	-35463

rs2298753

Genomic Coordinates

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

Population Frequency

P-Value

eQTL of rs2298753 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2298753 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)