rs2672213

Homo sapiens
C>T
CHRNA10 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0122 (3677/29948,GnomAD)
T=0128 (3744/29118,TOPMED)
T=0099 (498/5008,1000G)
T=0143 (550/3854,ALSPAC)
T=0147 (544/3708,TWINSUK)
chr11:3670187 (GRCh38.p7) (11p15.4)
AD
GWASdb2
2   publication(s)
See rs on genome
2 Enhancers around
7 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.3670187C>T
GRCh37.p13 chr 11NC_000011.9:g.3691417C>T

Gene: CHRNA10, cholinergic receptor nicotinic alpha 10 subunit(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CHRNA10 transcript variant 2NM_001303034.1:c.N/AIntron Variant
CHRNA10 transcript variant 3NM_001303035.1:c.N/AIntron Variant
CHRNA10 transcript variant 1NM_020402.3:c.N/AIntron Variant
CHRNA10 transcript variant X1XM_011520234.1:c.N/A5 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.930T=0.070
1000GenomesAmericanSub694C=0.820T=0.180
1000GenomesEast AsianSub1008C=0.974T=0.026
1000GenomesEuropeSub1006C=0.848T=0.152
1000GenomesGlobalStudy-wide5008C=0.901T=0.099
1000GenomesSouth AsianSub978C=0.900T=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.857T=0.143
The Genome Aggregation DatabaseAfricanSub8716C=0.936T=0.064
The Genome Aggregation DatabaseAmericanSub838C=0.840T=0.160
The Genome Aggregation DatabaseEast AsianSub1620C=0.960T=0.040
The Genome Aggregation DatabaseEuropeSub18472C=0.845T=0.155
The Genome Aggregation DatabaseGlobalStudy-wide29948C=0.877T=0.122
The Genome Aggregation DatabaseOtherSub302C=0.830T=0.170
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.871T=0.128
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.853T=0.147
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
17373692No evidence for association between 19 cholinergic genes and bipolar disorder.Shi JAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs26722130.00088alcohol dependence20201924

eQTL of rs2672213 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 rs2672213 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 )
chr1136455343645628E070-45789
chr1136458583645964E070-45453

Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1136629273664530E067-26887
chr1136629273664530E069-26887
chr1136627873662900E070-28517
chr1136629273664530E070-26887
chr1136629273664530E071-26887
chr1136629273664530E073-26887
chr1136629273664530E082-26887