rs1317286

Homo sapiens
A>G
CHRNA3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0296 (8862/29900,GnomAD)
G=0300 (8748/29118,TOPMED)
G=0222 (1111/5008,1000G)
G=0325 (1254/3854,ALSPAC)
G=0330 (1222/3708,TWINSUK)
chr15:78603787 (GRCh38.p7) (15q25.1)
ND
GWASdb2
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.78603787A>G
GRCh37.p13 chr 15NC_000015.9:g.78896129A>G
CHRNA3 RefSeqGeneNG_016143.1:g.22509T>C

Gene: CHRNA3, cholinergic receptor nicotinic alpha 3 subunit(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CHRNA3 transcript variant 1NM_000743.4:c.N/AIntron Variant
CHRNA3 transcript variant 2NM_001166694.1:c.N/AIntron Variant
CHRNA3 transcript variant 3NR_046313.1:n.N/AIntron Variant
CHRNA3 transcript variant X1XM_006720382.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.769G=0.231
1000GenomesAmericanSub694A=0.770G=0.230
1000GenomesEast AsianSub1008A=0.915G=0.085
1000GenomesEuropeSub1006A=0.628G=0.372
1000GenomesGlobalStudy-wide5008A=0.778G=0.222
1000GenomesSouth AsianSub978A=0.810G=0.190
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.675G=0.325
The Genome Aggregation DatabaseAfricanSub8698A=0.757G=0.243
The Genome Aggregation DatabaseAmericanSub838A=0.790G=0.210
The Genome Aggregation DatabaseEast AsianSub1616A=0.887G=0.113
The Genome Aggregation DatabaseEuropeSub18446A=0.659G=0.340
The Genome Aggregation DatabaseGlobalStudy-wide29900A=0.703G=0.296
The Genome Aggregation DatabaseOtherSub302A=0.630G=0.370
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.699G=0.300
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.670G=0.330
PMID Title Author Journal
21229299Chromosome 15q24-25.1 variants, diet, and lung cancer susceptibility in cigarette smokers.Sakoda LCCancer Causes Control
25036316Joint association of nicotinic acetylcholine receptor variants with abdominal obesity in American Indians: the Strong Heart Family Study.Zhu YPLoS One
18759969In search of causal variants: refining disease association signals using cross-population contrasts.Saccone NLBMC Genet
20808433Associations of variants in CHRNA5/A3/B4 gene cluster with smoking behaviors in a Korean population.Li MDPLoS One
22495174DRD1 associations with smoking abstinence across slow and normal nicotine metabolizers.Lee WPharmacogenet Genomics
23027417Nicotinic mechanisms in the treatment of psychotic disorders: a focus on the alpha7 nicotinic receptor.Olincy AHandb Exp Pharmacol
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
20554942Nicotinic acetylcholine receptor region on chromosome 15q25 and lung cancer risk among African Americans: a case-control study.Amos CIJ Natl Cancer Inst
19706762The CHRNA5-CHRNA3-CHRNB4 nicotinic receptor subunit gene cluster affects risk for nicotine dependence in African-Americans and in European-Americans.Saccone NLCancer Res
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
23429840Prepulse inhibition of startle response: recent advances in human studies of psychiatric disease.Takahashi HClin Psychopharmacol Neurosci
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
20393456Sensorimotor gating is associated with CHRNA3 polymorphisms in schizophrenia and healthy volunteers.Petrovsky NNeuropsychopharmacology
21808284Gender-stratified gene and gene-treatment interactions in smoking cessation.Lee WPharmacogenomics J
19259974Multiple distinct risk loci for nicotine dependence identified by dense coverage of the complete family of nicotinic receptor subunit (CHRN) genes.Saccone NLAm J Med Genet B Neuropsychiatr Genet
20548021Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium.Truong TJ Natl Cancer Inst
18571741Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research.Portugal GSBehav Brain Res
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
rs13172862.6E-06nicotine dependence18227835

eQTL of rs1317286 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:78896129CHRNA5ENSG00000169684.9A>G4.8140e-1738267Frontal_Cortex_BA9
Chr15:78896129CHRNA5ENSG00000169684.9A>G1.6230e-2038267Cortex
Chr15:78896129CHRNA5ENSG00000169684.9A>G1.5335e-1438267Caudate_basal_ganglia
Chr15:78896129RP11-650L12.2ENSG00000261762.1A>G1.2470e-1212511Caudate_basal_ganglia
Chr15:78896129CHRNA3ENSG00000080644.11A>G3.9747e-24-17508Caudate_basal_ganglia
Chr15:78896129CHRNA5ENSG00000169684.9A>G5.1270e-1538267Nucleus_accumbens_basal_ganglia

meQTL of rs1317286 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 )
chr157885686878857013E072-39116
chr157892992678929999E08133797
chr157893003378930244E08133904
chr157893454078934590E08138411
chr157893478278934896E08138653
chr157886578678866130E082-29999
chr157891955378919674E08223424
chr157891979978919961E08223670
chr157893003378930244E08233904
chr157893454078934590E08238411



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr157885705278859300E067-36829
chr157891174978913845E06815620
chr157885705278859300E069-36829
chr157893286278934267E06936733
chr157885705278859300E070-36829
chr157893286278934267E07036733
chr157893286278934267E07136733
chr157885705278859300E072-36829
chr157885705278859300E073-36829
chr157885705278859300E074-36829
chr157893286278934267E07436733
chr157885705278859300E081-36829
chr157885705278859300E082-36829
chr157891174978913845E08215620
chr157893271878932860E08236589
chr157893286278934267E08236733