rs578776

Homo sapiens
G>A
CHRNA3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0391 (11714/29950,GnomAD)
A=0414 (12071/29118,TOPMED)
G==0445 (2230/5008,1000G)
A=0291 (1122/3854,ALSPAC)
A=0277 (1027/3708,TWINSUK)
chr15:78596058 (GRCh38.p7) (15q25.1)
ND
GWASdb2
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.78596058G>A
GRCh37.p13 chr 15NC_000015.9:g.78888400G>A
CHRNA5 RefSeqGeneNG_023328.1:g.35539G>A
CHRNA3 RefSeqGeneNG_016143.1:g.30238C>T

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

Molecule type Change Amino acid[Codon] SO Term
CHRNA3 transcript variant 2NM_001166694.1:c.N/AIntron Variant
CHRNA3 transcript variant 1NM_000743.4:c.N/A3 Prime UTR Variant
CHRNA3 transcript variant 3NR_046313.1:n.N/AIntron Variant
CHRNA3 transcript variant X1XM_006720382.2:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.396A=0.604
1000GenomesAmericanSub694G=0.400A=0.600
1000GenomesEast AsianSub1008G=0.199A=0.801
1000GenomesEuropeSub1006G=0.719A=0.281
1000GenomesGlobalStudy-wide5008G=0.445A=0.555
1000GenomesSouth AsianSub978G=0.510A=0.490
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.709A=0.291
The Genome Aggregation DatabaseAfricanSub8714G=0.462A=0.538
The Genome Aggregation DatabaseAmericanSub838G=0.390A=0.610
The Genome Aggregation DatabaseEast AsianSub1620G=0.225A=0.775
The Genome Aggregation DatabaseEuropeSub18476G=0.720A=0.279
The Genome Aggregation DatabaseGlobalStudy-wide29950G=0.608A=0.391
The Genome Aggregation DatabaseOtherSub302G=0.690A=0.310
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.585A=0.414
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.723A=0.277
PMID Title Author Journal
19132693Variants in nicotinic acetylcholine receptors alpha5 and alpha3 increase risks to nicotine dependence.Chen XAm J Med Genet B Neuropsychiatr Genet
20624154Incorporating age at onset of smoking into genetic models for nicotine dependence: evidence for interaction with multiple genes.Grucza RAAddict Biol
23689675Genetic risk for nicotine dependence in the cholinergic system and activation of the brain reward system in healthy adolescents.Nees FNeuropsychopharmacology
21748402A twin association study of nicotine dependence with markers in the CHRNA3 and CHRNA5 genes.Maes HHBehav Genet
22046326'Smoking genes': a genetic association study.Verde ZPLoS One
18414406Genetic variation in the CHRNA5 gene affects mRNA levels and is associated with risk for alcohol dependence.Wang JCMol Psychiatry
19443489Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in CHRNA5.Wang JCHum Mol Genet
20808433Associations of variants in CHRNA5/A3/B4 gene cluster with smoking behaviors in a Korean population.Li MDPLoS One
24375168ADHD diagnosis may influence the association between polymorphisms in nicotinic acetylcholine receptor genes and tobacco smoking.Polina ERNeuromolecular Med
23143843Molecular mechanisms underlying behaviors related to nicotine addiction.Picciotto MRCold Spring Harb Perspect Med
20643934A genetically modulated, intrinsic cingulate circuit supports human nicotine addiction.Hong LEProc Natl Acad Sci U S A
20886544Risk gene variants for nicotine dependence in the CHRNA5-CHRNA3-CHRNB4 cluster are associated with cognitive performance.Winterer GAm J Med Genet B Neuropsychiatr Genet
19596527Nicotine dependence and genetic variation in the nicotinic receptors.Bierut LJDrug Alcohol Depend
17135278Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs.Saccone SFHum Mol Genet
24065931The CHRNA3 rs578776 Variant is Associated with an Intrinsic Reward Sensitivity Deficit in Smokers.Robinson JDFront Psychiatry
20393456Sensorimotor gating is associated with CHRNA3 polymorphisms in schizophrenia and healthy volunteers.Petrovsky NNeuropsychopharmacology
23397474Polymorphisms of CHRNA5-CHRNA3-CHRNB4 Gene Cluster and NSCLC Risk in Chinese Population.Li ZTransl Oncol
27166759Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions.Yang JMol Psychiatry
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
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
25632390Association between genetic variants on chromosome 15q25 locus and several nicotine dependence traits in Polish population: a case-control study.Buczkowski KBiomed Res Int
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
21606948Varenicline for smoking cessation: nausea severity and variation in nicotinic receptor genes.Swan GEPharmacogenomics J
25139936Association of cancer susceptibility variants with risk of multiple primary cancers: The population architecture using genomics and epidemiology study.Park SLCancer Epidemiol Biomarkers Prev
24588897CHRNA5 and CHRNA3 variants and level of neuroticism in young adult Mexican American men and women.Criado JRTwin Res Hum Genet
18783506Association of a single nucleotide polymorphism in neuronal acetylcholine receptor subunit alpha 5 (CHRNA5) with smoking status and with 'pleasurable buzz' during early experimentation with smoking.Sherva RAddiction
19184766A testable prognostic model of nicotine dependence.Ramoni RBJ Neurogenet
20736995Resequencing of nicotinic acetylcholine receptor genes and association of common and rare variants with the Fagerstrom test for nicotine dependence.Wessel JNeuropsychopharmacology
22992668Pharmacogenomics knowledge for personalized medicine.Whirl-Carrillo MClin Pharmacol Ther
19436041Human neuronal acetylcholine receptor A5-A3-B4 haplotypes are associated with multiple nicotine dependence phenotypes.Baker TBNicotine Tob Res
22832964Genome-wide meta-analyses of smoking behaviors in African Americans.David SPTransl Psychiatry
21191315Genetic association of bipolar disorder with the beta(3) nicotinic receptor subunit gene.Hartz SMPsychiatr Genet
26044620Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction.Reyes-Gibby CCBMC Syst Biol
24186853Distinct loci in the CHRNA5/CHRNA3/CHRNB4 gene cluster are associated with onset of regular smoking.Stephens SHGenet Epidemiol
20587604Fine mapping of chromosome 15q25.1 lung cancer susceptibility in African-Americans.Hansen HMHum Mol Genet
19247474Genome-wide and candidate gene association study of cigarette smoking behaviors.Caporaso NPLoS One
22438940Variants located upstream of CHRNB4 on chromosome 15q25.1 are associated with age at onset of daily smoking and habitual smoking.Kapoor MPLoS One
22539395Smoking and genetic risk variation across populations of European, Asian, and African American ancestry--a meta-analysis of chromosome 15q25.Chen LSGenet Epidemiol
25874685CHRNA3 rs6495308 genotype as an effect modifier of the association between daily cigarette consumption and hypertension in Chinese male smokers.Wu XYInt J Environ Res Public Health
25036316Joint association of nicotinic acetylcholine receptor variants with abdominal obesity in American Indians: the Strong Heart Family Study.Zhu YPLoS One
21559498Chromosome 15q25 (CHRNA3-CHRNA5) variation impacts indirectly on lung cancer risk.Wang YPLoS One
18618000A candidate gene approach identifies the CHRNA5-A3-B4 region as a risk factor for age-dependent nicotine addiction.Weiss RBPLoS Genet
20418888Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior.Thorgeirsson TENat Genet
26981579Gene by Environment Investigation of Incident Lung Cancer Risk in African-Americans.David SPEBioMedicine
20840187Peer smoking and the nicotinic receptor genes: an examination of genetic and environmental risks for nicotine dependence.Johnson EOAddiction
27197960Association between variants in nicotinic acetylcholine receptor genes and smoking cessation in a Chinese rural population.Wang QAm J Addict
21810735Single nucleotide polymorphisms in CHRNA5 rs16969968, CHRNA3 rs578776, and LOC123688 rs8034191 are associated with heaviness of smoking in women in Northeastern Ontario, Canada.Conlon MSNicotine Tob Res
22806211The genetics of addiction-a translational perspective.Agrawal ATransl Psychiatry
21385908Association of the nicotine metabolite ratio and CHRNA5/CHRNA3 polymorphisms with smoking rate among treatment-seeking smokers.Falcone MNicotine Tob Res
20631687Variation in the nicotinic acetylcholine receptor gene cluster CHRNA5-CHRNA3-CHRNB4 and its interaction with recent tobacco use influence cognitive flexibility.Zhang HNeuropsychopharmacology
21808284Gender-stratified gene and gene-treatment interactions in smoking cessation.Lee WPharmacogenomics J
25642160Nicotinic receptor modulation to treat alcohol and drug dependence.Rahman SFront Neurosci
18519524Variants in nicotinic receptors and risk for nicotine dependence.Bierut LJAm J Psychiatry
22176972Nicotinic acetylcholine receptor variants associated with susceptibility to chronic obstructive pulmonary disease: a meta-analysis.Zhang JRespir Res
18565990Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence.Saccone SFBioinformatics
26695521Mendelian Randomization - the Key to Understanding Aspects of Parkinson's Disease Causation?Noyce AJMov Disord
23692359CHRNA5-A3-B4 genetic variants alter nicotine intake and interact with tobacco use to influence body weight in Alaska Native tobacco users.Zhu AZAddiction
22048466Smoking cessation pharmacogenetics: analysis of varenicline and bupropion in placebo-controlled clinical trials.King DPNeuropsychopharmacology
18571741Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research.Portugal GSBehav Brain Res
26351737Nicotinic acetylcholine receptors: upregulation, age-related effects and associations with drug use.Melroy-Greif WEGenes Brain Behav
21229299Chromosome 15q24-25.1 variants, diet, and lung cancer susceptibility in cigarette smokers.Sakoda LCCancer Causes Control
22438921Nicotinic acetylcholine receptor variants are related to smoking habits, but not directly to COPD.Budulac SEPLoS One
23943838Effect of neuronal nicotinic acetylcholine receptor genes (CHRN) on longitudinal cigarettes per day in adolescents and young adults.Cannon DSNicotine Tob Res
20581870From smoking to lung cancer: the CHRNA5/A3/B4 connection.Improgo MROncogene
20700436Multiple independent loci at chromosome 15q25.1 affect smoking quantity: a meta-analysis and comparison with lung cancer and COPD.Saccone NLPLoS Genet
28069549SNPs within CHRNA5-A3-B4 and CYP2A6/B6 are associated with smoking dependence but not with tobacco dependence treatment outcomes in the Czech population.Hubacek JAGene
23872218Functional characterization of SNPs in CHRNA3/B4 intergenic region associated with drug behaviors.Flora AVBrain Res
23249876Nicotinic acetylcholine receptor variation and response to smoking cessation therapies.Bergen AWPharmacogenet Genomics
21228559An exploratory study on the CHRNA3-CHRNA5-CHRNB4 cluster, smoking, and Parkinson's disease.Gao JNeurodegener Dis
19706762The CHRNA5-CHRNA3-CHRNB4 nicotinic receptor subunit gene cluster affects risk for nicotine dependence in African-Americans and in European-Americans.Saccone NLCancer Res
21862624Genetic polymorphisms in 15q25 and 19q13 loci, cotinine levels, and risk of lung cancer in EPIC.Timofeeva MNCancer Epidemiol Biomarkers Prev
25045619The Genetics, Neurogenetics and Pharmacogenetics of Addiction.Demers CHCurr Behav Neurosci Rep
22042234Externalizing behaviors are associated with SNPs in the CHRNA5/CHRNA3/CHRNB4 gene cluster.Stephens SHBehav Genet
26010901Lack of Associations of CHRNA5-A3-B4 Genetic Variants with Smoking Cessation Treatment Outcomes in Caucasian Smokers despite Associations with Baseline Smoking.Tyndale RFPLoS One
21436384Genetic variability of smoking persistence in African Americans.Hamidovic ACancer Prev Res (Phila)
22291610A flexible Bayesian model for studying gene-environment interaction.Yu KPLoS Genet
21949713Genetics of sputum gene expression in chronic obstructive pulmonary disease.Qiu WPLoS One
18780872Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer.Liu PJ Natl Cancer Inst
22241830Analysis of detailed phenotype profiles reveals CHRNA5-CHRNA3-CHRNB4 gene cluster association with several nicotine dependence traits.Broms UNicotine Tob Res
25941207An Adolescent Substance Prevention Model Blocks the Effect of CHRNA5 Genotype on Smoking During High School.Vandenbergh DJNicotine Tob Res
25471942Contribution of Variants in CHRNA5/A3/B4 Gene Cluster on Chromosome 15 to Tobacco Smoking: From Genetic Association to Mechanism.Wen LMol Neurobiol
23875064Scrutiny of the CHRNA5-CHRNA3-CHRNB4 smoking behavior locus reveals a novel association with alcohol use in a Finnish population based study.Hallfors JInt J Mol Epidemiol Genet
23024249Development of novel pharmacotherapeutics for tobacco dependence: progress and future directions.Harmey DNicotine Tob Res
22884254Association of nicotine dependence susceptibility gene, CHRNA5, with Parkinson's disease age at onset: gene and smoking status interaction.Greenbaum LParkinsonism Relat Disord
23691092Associations of prenatal nicotine exposure and the dopamine related genes ANKK1 and DRD2 to verbal language.Eicher JDPLoS One
20700147Nicotinic alpha5 receptor subunit mRNA expression is associated with distant 5' upstream polymorphisms.Smith RMEur J Hum Genet
23255854A functional polymorphism in the CHRNA3 gene and risk of chronic obstructive pulmonary disease in a Korean population.Lee JYJ Korean Med Sci
27127891Association Between CHRNA3 and CHRNA5 Nicotine Receptor Subunit Gene Variants and Nicotine Dependence in an Isolated Populationof Kashubians in Poland.Kita-Milczarska KMed Sci Monit
20584212Multiple cholinergic nicotinic receptor genes affect nicotine dependence risk in African and European Americans.Saccone NLGenes Brain Behav
21685187Genome-wide association study of smoking behaviours in patients with COPD.Siedlinski MThorax
26831765Association between two CHRNA3 variants and susceptibility of lung cancer: a meta-analysis.Qu XSci Rep
19628476Association of serum cotinine level with a cluster of three nicotinic acetylcholine receptor genes (CHRNA3/CHRNA5/CHRNB4) on chromosome 15.Keskitalo KHum Mol Genet
19029397Nicotinic receptor gene variants influence susceptibility to heavy smoking.Stevens VLCancer Epidemiol Biomarkers Prev
25233467Role of nicotine dependence on the relationship between variants in the nicotinic receptor genes and risk of lung adenocarcinoma.Tseng TSPLoS One

P-Value

SNP ID p-value Traits Study
rs5787760.001Drug response to nicotine18618000

eQTL of rs578776 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:78888400RP11-650L12.2ENSG00000261762.1G>A4.4269e-64782Nucleus_accumbens_basal_ganglia
Chr15:78888400CHRNA3ENSG00000080644.11G>A7.4998e-13-25237Nucleus_accumbens_basal_ganglia

meQTL of rs578776 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 )
chr157885686878857013E072-31387
chr157892992678929999E08141526
chr157893003378930244E08141633
chr157893454078934590E08146140
chr157893478278934896E08146382
chr157886578678866130E082-22270
chr157891955378919674E08231153
chr157891979978919961E08231399
chr157893003378930244E08241633
chr157893454078934590E08246140



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr157885705278859300E067-29100
chr157891174978913845E06823349
chr157885705278859300E069-29100
chr157893286278934267E06944462
chr157885705278859300E070-29100
chr157893286278934267E07044462
chr157893286278934267E07144462
chr157885705278859300E072-29100
chr157885705278859300E073-29100
chr157885705278859300E074-29100
chr157893286278934267E07444462
chr157885705278859300E081-29100
chr157885705278859300E082-29100
chr157891174978913845E08223349
chr157893271878932860E08244318
chr157893286278934267E08244462