| Sequence Name | Change(s) |
|---|---|
| GRCh38.p7 chr 15 | NC_000015.10:g.78603787A>G |
| GRCh37.p13 chr 15 | NC_000015.9:g.78896129A>G |
| CHRNA3 RefSeqGene | NG_016143.1:g.22509T>C |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| CHRNA3 transcript variant 1 | NM_000743.4:c. | N/A | Intron Variant |
| CHRNA3 transcript variant 2 | NM_001166694.1:c. | N/A | Intron Variant |
| CHRNA3 transcript variant 3 | NR_046313.1:n. | N/A | Intron Variant |
| CHRNA3 transcript variant X1 | XM_006720382.2:c. | N/A | Intron Variant |
| Study | Population | Group | Sample # | Ref Allele | Alt Allele |
|---|---|---|---|---|---|
| 1000Genomes | African | Sub | 1322 | A=0.769 | G=0.231 |
| 1000Genomes | American | Sub | 694 | A=0.770 | G=0.230 |
| 1000Genomes | East Asian | Sub | 1008 | A=0.915 | G=0.085 |
| 1000Genomes | Europe | Sub | 1006 | A=0.628 | G=0.372 |
| 1000Genomes | Global | Study-wide | 5008 | A=0.778 | G=0.222 |
| 1000Genomes | South Asian | Sub | 978 | A=0.810 | G=0.190 |
| The Avon Longitudinal Study of Parents and Children | PARENT AND CHILD COHORT | Study-wide | 3854 | A=0.675 | G=0.325 |
| The Genome Aggregation Database | African | Sub | 8698 | A=0.757 | G=0.243 |
| The Genome Aggregation Database | American | Sub | 838 | A=0.790 | G=0.210 |
| The Genome Aggregation Database | East Asian | Sub | 1616 | A=0.887 | G=0.113 |
| The Genome Aggregation Database | Europe | Sub | 18446 | A=0.659 | G=0.340 |
| The Genome Aggregation Database | Global | Study-wide | 29900 | A=0.703 | G=0.296 |
| The Genome Aggregation Database | Other | Sub | 302 | A=0.630 | G=0.370 |
| Trans-Omics for Precision Medicine | Global | Study-wide | 29118 | A=0.699 | G=0.300 |
| UK 10K study - Twins | TWIN COHORT | Study-wide | 3708 | A=0.670 | G=0.330 |
| PMID | Title | Author | Journal |
|---|---|---|---|
| 21229299 | Chromosome 15q24-25.1 variants, diet, and lung cancer susceptibility in cigarette smokers. | Sakoda LC | Cancer Causes Control |
| 25036316 | Joint association of nicotinic acetylcholine receptor variants with abdominal obesity in American Indians: the Strong Heart Family Study. | Zhu Y | PLoS One |
| 18759969 | In search of causal variants: refining disease association signals using cross-population contrasts. | Saccone NL | BMC Genet |
| 20808433 | Associations of variants in CHRNA5/A3/B4 gene cluster with smoking behaviors in a Korean population. | Li MD | PLoS One |
| 22495174 | DRD1 associations with smoking abstinence across slow and normal nicotine metabolizers. | Lee W | Pharmacogenet Genomics |
| 23027417 | Nicotinic mechanisms in the treatment of psychotic disorders: a focus on the alpha7 nicotinic receptor. | Olincy A | Handb Exp Pharmacol |
| 19859904 | Association and interaction analysis of variants in CHRNA5/CHRNA3/CHRNB4 gene cluster with nicotine dependence in African and European Americans. | Li MD | Am J Med Genet B Neuropsychiatr Genet |
| 18227835 | Alpha-5/alpha-3 nicotinic receptor subunit alleles increase risk for heavy smoking. | Berrettini W | Mol Psychiatry |
| 20554942 | Nicotinic acetylcholine receptor region on chromosome 15q25 and lung cancer risk among African Americans: a case-control study. | Amos CI | J Natl Cancer Inst |
| 19706762 | The CHRNA5-CHRNA3-CHRNB4 nicotinic receptor subunit gene cluster affects risk for nicotine dependence in African-Americans and in European-Americans. | Saccone NL | Cancer Res |
| 19330903 | Gene by smoking interaction in hypertension: identification of a major quantitative trait locus on chromosome 15q for systolic blood pressure in Mexican-Americans. | Montasser ME | J Hypertens |
| 23429840 | Prepulse inhibition of startle response: recent advances in human studies of psychiatric disease. | Takahashi H | Clin Psychopharmacol Neurosci |
| 22837378 | Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction. | Wilk JB | Am J Respir Crit Care Med |
| 19443489 | Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in CHRNA5. | Wang JC | Hum Mol Genet |
| 20393456 | Sensorimotor gating is associated with CHRNA3 polymorphisms in schizophrenia and healthy volunteers. | Petrovsky N | Neuropsychopharmacology |
| 21808284 | Gender-stratified gene and gene-treatment interactions in smoking cessation. | Lee W | Pharmacogenomics J |
| 19259974 | Multiple distinct risk loci for nicotine dependence identified by dense coverage of the complete family of nicotinic receptor subunit (CHRN) genes. | Saccone NL | Am J Med Genet B Neuropsychiatr Genet |
| 20548021 | Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. | Truong T | J Natl Cancer Inst |
| 18571741 | Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. | Portugal GS | Behav Brain Res |
| 25051068 | Four SNPs in the CHRNA3/5 alpha-neuronal nicotinic acetylcholine receptor subunit locus are associated with COPD risk based on meta-analyses. | Cui K | PLoS One |
| SNP ID | p-value | Traits | Study |
|---|---|---|---|
| rs1317286 | 2.6E-06 | nicotine dependence | 18227835 |
| Position (v37) | eGene | GeneID | Variant | p-value | TSS | Tissue |
|---|---|---|---|---|---|---|
| Chr15:78896129 | CHRNA5 | ENSG00000169684.9 | A>G | 4.8140e-17 | 38267 | Frontal_Cortex_BA9 |
| Chr15:78896129 | CHRNA5 | ENSG00000169684.9 | A>G | 1.6230e-20 | 38267 | Cortex |
| Chr15:78896129 | CHRNA5 | ENSG00000169684.9 | A>G | 1.5335e-14 | 38267 | Caudate_basal_ganglia |
| Chr15:78896129 | RP11-650L12.2 | ENSG00000261762.1 | A>G | 1.2470e-12 | 12511 | Caudate_basal_ganglia |
| Chr15:78896129 | CHRNA3 | ENSG00000080644.11 | A>G | 3.9747e-24 | -17508 | Caudate_basal_ganglia |
| Chr15:78896129 | CHRNA5 | ENSG00000169684.9 | A>G | 5.1270e-15 | 38267 | Nucleus_accumbens_basal_ganglia |
| Probe ID | Position | Gene | beta | p-value | |||
|---|---|---|---|---|---|---|---|
| There is no meQTL annotation for this SNP | |||||||
There is no significant Hi-C chromatin interaction data for this SNP.
| Chromosome | Start | End | Region | Distance ( -/+ : Up/Downstream ) |
|---|---|---|---|---|
| chr15 | 78856868 | 78857013 | E072 | -39116 |
| chr15 | 78929926 | 78929999 | E081 | 33797 |
| chr15 | 78930033 | 78930244 | E081 | 33904 |
| chr15 | 78934540 | 78934590 | E081 | 38411 |
| chr15 | 78934782 | 78934896 | E081 | 38653 |
| chr15 | 78865786 | 78866130 | E082 | -29999 |
| chr15 | 78919553 | 78919674 | E082 | 23424 |
| chr15 | 78919799 | 78919961 | E082 | 23670 |
| chr15 | 78930033 | 78930244 | E082 | 33904 |
| chr15 | 78934540 | 78934590 | E082 | 38411 |
| Chromosome | Start | End | Region | Distance(-/+:Up/Downstream) |
|---|---|---|---|---|
| chr15 | 78857052 | 78859300 | E067 | -36829 |
| chr15 | 78911749 | 78913845 | E068 | 15620 |
| chr15 | 78857052 | 78859300 | E069 | -36829 |
| chr15 | 78932862 | 78934267 | E069 | 36733 |
| chr15 | 78857052 | 78859300 | E070 | -36829 |
| chr15 | 78932862 | 78934267 | E070 | 36733 |
| chr15 | 78932862 | 78934267 | E071 | 36733 |
| chr15 | 78857052 | 78859300 | E072 | -36829 |
| chr15 | 78857052 | 78859300 | E073 | -36829 |
| chr15 | 78857052 | 78859300 | E074 | -36829 |
| chr15 | 78932862 | 78934267 | E074 | 36733 |
| chr15 | 78857052 | 78859300 | E081 | -36829 |
| chr15 | 78857052 | 78859300 | E082 | -36829 |
| chr15 | 78911749 | 78913845 | E082 | 15620 |
| chr15 | 78932718 | 78932860 | E082 | 36589 |
| chr15 | 78932862 | 78934267 | E082 | 36733 |