rs951266

Homo sapiens
G>A
CHRNA5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0250 (7484/29918,GnomAD)
A=0233 (6804/29118,TOPMED)
A=0163 (817/5008,1000G)
A=0323 (1244/3854,ALSPAC)
A=0326 (1210/3708,TWINSUK)
chr15:78586199 (GRCh38.p7) (15q25.1)
ND
GWASdb2
23   publication(s)
See rs on genome
17 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.78586199G>A
GRCh37.p13 chr 15NC_000015.9:g.78878541G>A
CHRNA5 RefSeqGeneNG_023328.1:g.25680G>A

Gene: CHRNA5, cholinergic receptor nicotinic alpha 5 subunit(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CHRNA5 transcript variant 1NM_000745.3:c.N/AIntron Variant
CHRNA5 transcript variant 2NM_001307945.1:c.N/AIntron Variant
CHRNA5 transcript variant X3XM_005254142.3:c.N/AIntron Variant
CHRNA5 transcript variant X2XM_017021881.1:c.N/AIntron Variant
CHRNA5 transcript variant X1XR_001751067.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.927A=0.073
1000GenomesAmericanSub694G=0.790A=0.210
1000GenomesEast AsianSub1008G=0.973A=0.027
1000GenomesEuropeSub1006G=0.634A=0.366
1000GenomesGlobalStudy-wide5008G=0.837A=0.163
1000GenomesSouth AsianSub978G=0.820A=0.180
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.677A=0.323
The Genome Aggregation DatabaseAfricanSub8706G=0.893A=0.107
The Genome Aggregation DatabaseAmericanSub838G=0.790A=0.210
The Genome Aggregation DatabaseEast AsianSub1620G=0.971A=0.029
The Genome Aggregation DatabaseEuropeSub18452G=0.662A=0.337
The Genome Aggregation DatabaseGlobalStudy-wide29918G=0.749A=0.250
The Genome Aggregation DatabaseOtherSub302G=0.670A=0.330
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.766A=0.233
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.674A=0.326
PMID Title Author Journal
26981579Gene by Environment Investigation of Incident Lung Cancer Risk in African-Americans.David SPEBioMedicine
18759969In search of causal variants: refining disease association signals using cross-population contrasts.Saccone NLBMC Genet
27099524Natural killer cells and single nucleotide polymorphisms of specific ion channels and receptor genes in myalgic encephalomyelitis/chronic fatigue syndrome.Marshall-Gradisnik SAppl Clin Genet
19859904Association and interaction analysis of variants in CHRNA5/CHRNA3/CHRNB4 gene cluster with nicotine dependence in African and European Americans.Li MDAm J Med Genet B Neuropsychiatr Genet
18227835Alpha-5/alpha-3 nicotinic receptor subunit alleles increase risk for heavy smoking.Berrettini WMol Psychiatry
22837378Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.Wilk JBAm J Respir Crit Care Med
19443489Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in CHRNA5.Wang JCHum Mol Genet
23196875Variants in the 15q25 gene cluster are associated with risk for schizophrenia and bipolar disorder.Jackson KJPsychiatr Genet
25036316Joint association of nicotinic acetylcholine receptor variants with abdominal obesity in American Indians: the Strong Heart Family Study.Zhu YPLoS One
27694844An Adaptive Fisher's Combination Method for Joint Analysis of Multiple Phenotypes in Association Studies.Liang XSci Rep
20808433Associations of variants in CHRNA5/A3/B4 gene cluster with smoking behaviors in a Korean population.Li MDPLoS One
19330903Gene by smoking interaction in hypertension: identification of a major quantitative trait locus on chromosome 15q for systolic blood pressure in Mexican-Americans.Montasser MEJ Hypertens
22539395Smoking and genetic risk variation across populations of European, Asian, and African American ancestry--a meta-analysis of chromosome 15q25.Chen LSGenet Epidemiol
22648373Interplay of genetic risk factors (CHRNA5-CHRNA3-CHRNB4) and cessation treatments in smoking cessation success.Chen LSAm J Psychiatry
20700147Nicotinic alpha5 receptor subunit mRNA expression is associated with distant 5' upstream polymorphisms.Smith RMEur J Hum Genet
22899653Influence of common genetic variation on lung cancer risk: meta-analysis of 14 900 cases and 29 485 controls.Timofeeva MNHum Mol Genet
17373692No evidence for association between 19 cholinergic genes and bipolar disorder.Shi JAm J Med Genet B Neuropsychiatr Genet
23221128Fine-mapping of the 5p15.33, 6p22.1-p21.31, and 15q25.1 regions identifies functional and histology-specific lung cancer susceptibility loci in African-Americans.Walsh KMCancer Epidemiol Biomarkers Prev
27166759Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions.Yang JMol Psychiatry
18618000A candidate gene approach identifies the CHRNA5-A3-B4 region as a risk factor for age-dependent nicotine addiction.Weiss RBPLoS Genet
19706762The CHRNA5-CHRNA3-CHRNB4 nicotinic receptor subunit gene cluster affects risk for nicotine dependence in African-Americans and in European-Americans.Saccone NLCancer Res
20485328Variation in nicotinic acetylcholine receptor genes is associated with multiple substance dependence phenotypes.Sherva RNeuropsychopharmacology
25051068Four SNPs in the CHRNA3/5 alpha-neuronal nicotinic acetylcholine receptor subunit locus are associated with COPD risk based on meta-analyses.Cui KPLoS One

P-Value

SNP ID p-value Traits Study
rs9512660.0006nicotine dependence18227835

eQTL of rs951266 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:78878541CHRNA5ENSG00000169684.9G>A4.8140e-1720679Frontal_Cortex_BA9
Chr15:78878541CHRNA5ENSG00000169684.9G>A1.6230e-2020679Cortex
Chr15:78878541CHRNA5ENSG00000169684.9G>A1.5335e-1420679Caudate_basal_ganglia
Chr15:78878541RP11-650L12.2ENSG00000261762.1G>A1.2470e-12-5077Caudate_basal_ganglia
Chr15:78878541CHRNA3ENSG00000080644.11G>A3.9747e-24-35096Caudate_basal_ganglia
Chr15:78878541CHRNA5ENSG00000169684.9G>A2.5847e-520679Substantia_nigra
Chr15:78878541CHRNA5ENSG00000169684.9G>A1.0285e-1120679Anterior_cingulate_cortex
Chr15:78878541CHRNA5ENSG00000169684.9G>A5.1270e-1520679Nucleus_accumbens_basal_ganglia

meQTL of rs951266 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 )
chr157883465278834702E067-43839
chr157883465278834702E069-43839
chr157883485878834908E069-43633
chr157883506878835124E069-43417
chr157883512578835267E069-43274
chr157883541478835508E069-43033
chr157883557978835628E069-42913
chr157883465278834702E070-43839
chr157885686878857013E072-21528
chr157883465278834702E073-43839
chr157883465278834702E081-43839
chr157883485878834908E081-43633
chr157883465278834702E082-43839
chr157883485878834908E082-43633
chr157886578678866130E082-12411
chr157891955378919674E08241012
chr157891979978919961E08241258







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr157883216578832234E067-46307
chr157883228778834159E067-44382
chr157885705278859300E067-19241
chr157883216578832234E068-46307
chr157883228778834159E068-44382
chr157891174978913845E06833208
chr157883216578832234E069-46307
chr157883228778834159E069-44382
chr157885705278859300E069-19241
chr157883216578832234E070-46307
chr157883228778834159E070-44382
chr157885705278859300E070-19241
chr157883216578832234E071-46307
chr157883228778834159E071-44382
chr157883216578832234E072-46307
chr157883228778834159E072-44382
chr157885705278859300E072-19241
chr157883216578832234E073-46307
chr157883228778834159E073-44382
chr157885705278859300E073-19241
chr157883216578832234E074-46307
chr157883228778834159E074-44382
chr157885705278859300E074-19241
chr157883228778834159E081-44382
chr157885705278859300E081-19241
chr157883216578832234E082-46307
chr157883228778834159E082-44382
chr157885705278859300E082-19241
chr157891174978913845E08233208