rs680244

Homo sapiens
T>C
CHRNA5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0410 (12269/29880,GnomAD)
T==0406 (11833/29118,TOPMED)
T==0329 (1648/5008,1000G)
T==0445 (1715/3854,ALSPAC)
T==0450 (1670/3708,TWINSUK)
chr15:78578946 (GRCh38.p7) (15q25.1)
ND
GWASdb2
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.78578946T>C
GRCh37.p13 chr 15NC_000015.9:g.78871288T>C
CHRNA5 RefSeqGeneNG_023328.1:g.18427T>C

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
1000GenomesAfricanSub1322T=0.396C=0.604
1000GenomesAmericanSub694T=0.220C=0.780
1000GenomesEast AsianSub1008T=0.230C=0.770
1000GenomesEuropeSub1006T=0.390C=0.610
1000GenomesGlobalStudy-wide5008T=0.329C=0.671
1000GenomesSouth AsianSub978T=0.360C=0.640
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.445C=0.555
The Genome Aggregation DatabaseAfricanSub8694T=0.430C=0.570
The Genome Aggregation DatabaseAmericanSub836T=0.220C=0.780
The Genome Aggregation DatabaseEast AsianSub1618T=0.283C=0.717
The Genome Aggregation DatabaseEuropeSub18430T=0.421C=0.578
The Genome Aggregation DatabaseGlobalStudy-wide29880T=0.410C=0.589
The Genome Aggregation DatabaseOtherSub302T=0.400C=0.600
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.406C=0.593
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.450C=0.550
PMID Title Author Journal
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
25214750Genomics and personalized medicine: CHRNA5-CHRNA3-CHRNB4 and smoking cessation treatment.Chen LSJ Food Drug Anal
25819021A review of pharmacogenetic studies of substance-related disorders.Jones JDDrug Alcohol Depend
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
21079997Uncovering hidden variance: pair-wise SNP analysis accounts for additional variance in nicotine dependence.Culverhouse RCHum Genet
22382757The CHRNA5/A3/B4 gene cluster and tobacco, alcohol, cannabis, inhalants and other substance use initiation: replication and new findings using mixture analyses.Lubke GHBehav Genet
19064933Chromosome 15q25.1 genetic markers associated with level of response to alcohol in humans.Joslyn GProc Natl Acad Sci U S A
24588897CHRNA5 and CHRNA3 variants and level of neuroticism in young adult Mexican American men and women.Criado JRTwin Res Hum Genet
22291610A flexible Bayesian model for studying gene-environment interaction.Yu KPLoS Genet
16314871Why do young women smoke? I. Direct and interactive effects of environment, psychological characteristics and nicotinic cholinergic receptor genes.Greenbaum LMol Psychiatry
21268243Markers in the 15q24 nicotinic receptor subunit gene cluster (CHRNA5-A3-B4) predict severity of nicotine addiction and response to smoking cessation therapy.Sarginson JEAm J Med Genet B Neuropsychiatr Genet
25642160Nicotinic receptor modulation to treat alcohol and drug dependence.Rahman SFront Neurosci
20854418CHRNB2 promoter region: association with subjective effects to nicotine and gene expression differences.Hoft NRGenes Brain Behav
18519524Variants in nicotinic receptors and risk for nicotine dependence.Bierut LJAm J Psychiatry
23689675Genetic risk for nicotine dependence in the cholinergic system and activation of the brain reward system in healthy adolescents.Nees FNeuropsychopharmacology
21949713Genetics of sputum gene expression in chronic obstructive pulmonary disease.Qiu WPLoS One
19436041Human neuronal acetylcholine receptor A5-A3-B4 haplotypes are associated with multiple nicotine dependence phenotypes.Baker TBNicotine Tob Res
18414406Genetic variation in the CHRNA5 gene affects mRNA levels and is associated with risk for alcohol dependence.Wang JCMol Psychiatry
25233467Role of nicotine dependence on the relationship between variants in the nicotinic receptor genes and risk of lung adenocarcinoma.Tseng TSPLoS One
19443489Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in CHRNA5.Wang JCHum Mol 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
25572450Response to Transdermal Selegiline Smoking Cessation Therapy and Markers in the 15q24 Chromosomal Region.Sarginson JENicotine Tob Res
18163978The CHRNA5/A3/B4 gene cluster variability as an important determinant of early alcohol and tobacco initiation in young adults.Schlaepfer IRBiol Psychiatry
22290489Pharmacogenetics of smoking cessation: role of nicotine target and metabolism genes.Gold ABHum Genet
22241830Analysis of detailed phenotype profiles reveals CHRNA5-CHRNA3-CHRNB4 gene cluster association with several nicotine dependence traits.Broms UNicotine Tob Res
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
24055496A glimpse into the future - Personalized medicine for smoking cessation.Bierut LJNeuropharmacology
20554942Nicotinic acetylcholine receptor region on chromosome 15q25 and lung cancer risk among African Americans: a case-control study.Amos CIJ Natl Cancer Inst
23029550Associations between variation in CHRNA5-CHRNA3-CHRNB4, body mass index and blood pressure in the Northern Finland Birth Cohort 1966.Kaakinen MPLoS One
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
20700436Multiple independent loci at chromosome 15q25.1 affect smoking quantity: a meta-analysis and comparison with lung cancer and COPD.Saccone NLPLoS Genet
17373692No evidence for association between 19 cholinergic genes and bipolar disorder.Shi JAm J Med Genet B Neuropsychiatr 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
19628476Association of serum cotinine level with a cluster of three nicotinic acetylcholine receptor genes (CHRNA3/CHRNA5/CHRNB4) on chromosome 15.Keskitalo KHum Mol Genet
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
21168125TTC12-ANKK1-DRD2 and CHRNA5-CHRNA3-CHRNB4 influence different pathways leading to smoking behavior from adolescence to mid-adulthood.Ducci FBiol Psychiatry

P-Value

SNP ID p-value Traits Study
rs6802440.001Drug response to nicotine18618000

eQTL of rs680244 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:78871288CHRNA5ENSG00000169684.9T>C9.6445e-613426Cerebellum
Chr15:78871288CHRNA5ENSG00000169684.9T>C4.8140e-1713426Frontal_Cortex_BA9
Chr15:78871288CHRNA5ENSG00000169684.9T>C1.2801e-1013426Hypothalamus
Chr15:78871288CHRNA5ENSG00000169684.9T>C1.6230e-2013426Cortex
Chr15:78871288CHRNA5ENSG00000169684.9T>C1.2536e-513426Cerebellar_Hemisphere
Chr15:78871288CHRNA5ENSG00000169684.9T>C1.5335e-1413426Caudate_basal_ganglia
Chr15:78871288RP11-650L12.2ENSG00000261762.1T>C1.2470e-12-12330Caudate_basal_ganglia
Chr15:78871288CHRNA3ENSG00000080644.11T>C3.9747e-24-42349Caudate_basal_ganglia
Chr15:78871288CHRNA5ENSG00000169684.9T>C1.2511e-713426Brain_Spinal_cord_cervical
Chr15:78871288CHRNA5ENSG00000169684.9T>C7.7570e-1313426Hippocampus
Chr15:78871288CHRNA5ENSG00000169684.9T>C2.5847e-513426Substantia_nigra
Chr15:78871288PSMA4ENSG00000041357.11T>C3.0200e-338541Putamen_basal_ganglia
Chr15:78871288CHRNA5ENSG00000169684.9T>C1.9380e-1213426Putamen_basal_ganglia
Chr15:78871288RP11-650L12.2ENSG00000261762.1T>C2.8678e-8-12330Putamen_basal_ganglia
Chr15:78871288CHRNA3ENSG00000080644.11T>C7.5094e-15-42349Putamen_basal_ganglia
Chr15:78871288CHRNA5ENSG00000169684.9T>C1.0285e-1113426Anterior_cingulate_cortex
Chr15:78871288PSMA4ENSG00000041357.11T>C2.9136e-438541Nucleus_accumbens_basal_ganglia
Chr15:78871288CHRNA5ENSG00000169684.9T>C5.1270e-1513426Nucleus_accumbens_basal_ganglia
Chr15:78871288CHRNA3ENSG00000080644.11T>C7.4998e-13-42349Nucleus_accumbens_basal_ganglia
Chr15:78871288CHRNA5ENSG00000169684.9T>C5.4596e-813426Amygdala

meQTL of rs680244 in Fetal Brain

Probe ID Position Gene beta p-value
cg06917634chr15:78832804PSMA40.0075228991099853.2042e-15
cg06917634chr15:78832804PSMA40.0075228993.2000e-15

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 )
chr157883465278834702E067-36586
chr157883465278834702E069-36586
chr157883485878834908E069-36380
chr157883506878835124E069-36164
chr157883512578835267E069-36021
chr157883541478835508E069-35780
chr157883557978835628E069-35660
chr157883465278834702E070-36586
chr157885686878857013E072-14275
chr157883465278834702E073-36586
chr157883465278834702E081-36586
chr157883485878834908E081-36380
chr157883465278834702E082-36586
chr157883485878834908E082-36380
chr157886578678866130E082-5158
chr157891955378919674E08248265
chr157891979978919961E08248511







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr157883216578832234E067-39054
chr157883228778834159E067-37129
chr157885705278859300E067-11988
chr157883216578832234E068-39054
chr157883228778834159E068-37129
chr157891174978913845E06840461
chr157883216578832234E069-39054
chr157883228778834159E069-37129
chr157885705278859300E069-11988
chr157883216578832234E070-39054
chr157883228778834159E070-37129
chr157885705278859300E070-11988
chr157883216578832234E071-39054
chr157883228778834159E071-37129
chr157883216578832234E072-39054
chr157883228778834159E072-37129
chr157885705278859300E072-11988
chr157883216578832234E073-39054
chr157883228778834159E073-37129
chr157885705278859300E073-11988
chr157883216578832234E074-39054
chr157883228778834159E074-37129
chr157885705278859300E074-11988
chr157883228778834159E081-37129
chr157885705278859300E081-11988
chr157883216578832234E082-39054
chr157883228778834159E082-37129
chr157885705278859300E082-11988
chr157891174978913845E08240461