rs6495308

Homo sapiens
T>C
CHRNA3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0290 (8687/29882,GnomAD)
C=0283 (8251/29118,TOPMED)
C=0449 (2251/5008,1000G)
C=0235 (904/3854,ALSPAC)
C=0221 (818/3708,TWINSUK)
chr15:78615314 (GRCh38.p7) (15q25.1)
ND
GWASdb2
See rs on genome
9 Enhancers around
8 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.78615314T>C
GRCh37.p13 chr 15NC_000015.9:g.78907656T>C
CHRNA3 RefSeqGeneNG_016143.1:g.10982A>G

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
1000GenomesAfricanSub1322T=0.676C=0.324
1000GenomesAmericanSub694T=0.450C=0.550
1000GenomesEast AsianSub1008T=0.267C=0.733
1000GenomesEuropeSub1006T=0.759C=0.241
1000GenomesGlobalStudy-wide5008T=0.551C=0.449
1000GenomesSouth AsianSub978T=0.530C=0.470
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.765C=0.235
The Genome Aggregation DatabaseAfricanSub8704T=0.701C=0.299
The Genome Aggregation DatabaseAmericanSub836T=0.430C=0.570
The Genome Aggregation DatabaseEast AsianSub1616T=0.316C=0.684
The Genome Aggregation DatabaseEuropeSub18424T=0.759C=0.240
The Genome Aggregation DatabaseGlobalStudy-wide29882T=0.709C=0.290
The Genome Aggregation DatabaseOtherSub302T=0.720C=0.280
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.716C=0.283
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.779C=0.221
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
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
27827986Replicated Risk Nicotinic Cholinergic Receptor Genes for Nicotine Dependence.Zuo LGenes (Basel)
23143843Molecular mechanisms underlying behaviors related to nicotine addiction.Picciotto MRCold Spring Harb Perspect Med
18519524Variants in nicotinic receptors and risk for nicotine dependence.Bierut LJAm J Psychiatry
21748402A twin association study of nicotine dependence with markers in the CHRNA3 and CHRNA5 genes.Maes HHBehav Genet
18165968Identification of pharmacogenetic markers in smoking cessation therapy.Heitjan DFAm J Med Genet B Neuropsychiatr Genet
26695521Mendelian Randomization - the Key to Understanding Aspects of Parkinson's Disease Causation?Noyce AJMov Disord
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
23692359CHRNA5-A3-B4 genetic variants alter nicotine intake and interact with tobacco use to influence body weight in Alaska Native tobacco users.Zhu AZAddiction
18571741Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research.Portugal GSBehav Brain Res
24339136Neurophysiologic effect of GWAS derived schizophrenia and bipolar risk variants.Hall MHAm J Med Genet B Neuropsychiatr Genet
22544838From men to mice: CHRNA5/CHRNA3, smoking behavior and disease.Ware JJNicotine Tob Res
25632390Association between genetic variants on chromosome 15q25 locus and several nicotine dependence traits in Polish population: a case-control study.Buczkowski KBiomed Res Int
22899653Influence of common genetic variation on lung cancer risk: meta-analysis of 14 900 cases and 29 485 controls.Timofeeva MNHum Mol Genet
20808433Associations of variants in CHRNA5/A3/B4 gene cluster with smoking behaviors in a Korean population.Li MDPLoS One
23943838Effect of neuronal nicotinic acetylcholine receptor genes (CHRN) on longitudinal cigarettes per day in adolescents and young adults.Cannon DSNicotine Tob Res
22223462Alpha-5 and -3 nicotinic receptor gene variants predict nicotine dependence but not cessation: findings from the COMMIT cohort.Bousman CAAm J Med Genet B Neuropsychiatr Genet
26942719Chromosome 15q25 (CHRNA3-CHRNB4) Variation Indirectly Impacts Lung Cancer Risk in Chinese Males.Zhang YPLoS One
23024249Development of novel pharmacotherapeutics for tobacco dependence: progress and future directions.Harmey DNicotine Tob Res
19741265Genetics and genomics of chronic obstructive pulmonary disease.Silverman EKProc Am Thorac Soc
23536134Polygenic risk and the developmental progression to heavy, persistent smoking and nicotine dependence: evidence from a 4-decade longitudinal study.Belsky DWJAMA Psychiatry
22539395Smoking and genetic risk variation across populations of European, Asian, and African American ancestry--a meta-analysis of chromosome 15q25.Chen LSGenet Epidemiol
23691092Associations of prenatal nicotine exposure and the dopamine related genes ANKK1 and DRD2 to verbal language.Eicher JDPLoS One
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
20418889Meta-analysis and imputation refines the association of 15q25 with smoking quantity.Liu JZNat Genet
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
20700436Multiple independent loci at chromosome 15q25.1 affect smoking quantity: a meta-analysis and comparison with lung cancer and COPD.Saccone NLPLoS Genet
26948517Genetic scores of smoking behaviour in a Chinese population.Yang SSci Rep
22102793GENES AS INSTRUMENTS FOR STUDYING RISK BEHAVIOR EFFECTS: AN APPLICATION TO MATERNAL SMOKING AND OROFACIAL CLEFTS.Wehby GHealth Serv Outcomes Res Methodol
20393456Sensorimotor gating is associated with CHRNA3 polymorphisms in schizophrenia and healthy volunteers.Petrovsky NNeuropsychopharmacology
27335628A prospective and retrospective analysis of smoking behavior changes in ever smokers with high risk for lung cancer from New Mexico and Pennsylvania.Leng SInt J Mol Epidemiol Genet
25036316Joint association of nicotinic acetylcholine receptor variants with abdominal obesity in American Indians: the Strong Heart Family Study.Zhu YPLoS One
27166759Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions.Yang JMol Psychiatry
20736995Resequencing of nicotinic acetylcholine receptor genes and association of common and rare variants with the Fagerstrom test for nicotine dependence.Wessel JNeuropsychopharmacology
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
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

P-Value

SNP ID p-value Traits Study
rs64953086.9E-05nicotine dependence18227835

eQTL of rs6495308 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:78907656CHRNA5ENSG00000169684.9T>C1.9380e-1249794Putamen_basal_ganglia
Chr15:78907656CHRNA3ENSG00000080644.11T>C7.4998e-13-5981Nucleus_accumbens_basal_ganglia

meQTL of rs6495308 in Fetal Brain

Probe ID Position Gene beta p-value
cg24631222chr15:78858424CHRNA50.02672678353613945.1881e-10

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 )
chr157892992678929999E08122270
chr157893003378930244E08122377
chr157893454078934590E08126884
chr157893478278934896E08127126
chr157886578678866130E082-41526
chr157891955378919674E08211897
chr157891979978919961E08212143
chr157893003378930244E08222377
chr157893454078934590E08226884


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr157891174978913845E0684093
chr157893286278934267E06925206
chr157893286278934267E07025206
chr157893286278934267E07125206
chr157893286278934267E07425206
chr157891174978913845E0824093
chr157893271878932860E08225062
chr157893286278934267E08225206