rs569207

Homo sapiens
C>T
CHRNA5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0332 (37571/113108,ExAC)
T=0272 (8147/29858,GnomAD)
T=0272 (7941/29118,TOPMED)
C==0242 (3141/12976,GO-ESP)
T=0395 (1976/5008,1000G)
T=0230 (887/3854,ALSPAC)
T=0223 (826/3708,TWINSUK)
chr15:78580777 (GRCh38.p7) (15q25.1)
ND
GWASdb2
21   publication(s)
See rs on genome
17 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.78580777C>T
GRCh37.p13 chr 15NC_000015.9:g.78873119C>T
CHRNA5 RefSeqGeneNG_023328.1:g.20258C>T

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
1000GenomesAfricanSub1322C=0.684T=0.316
1000GenomesAmericanSub694C=0.440T=0.560
1000GenomesEast AsianSub1008C=0.519T=0.481
1000GenomesEuropeSub1006C=0.755T=0.245
1000GenomesGlobalStudy-wide5008C=0.605T=0.395
1000GenomesSouth AsianSub978C=0.550T=0.450
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.770T=0.230
The Exome Aggregation ConsortiumAmericanSub21092C=0.505T=0.495
The Exome Aggregation ConsortiumAsianSub22068C=0.534T=0.465
The Exome Aggregation ConsortiumEuropeSub69092C=0.760T=0.239
The Exome Aggregation ConsortiumGlobalStudy-wide113108C=0.667T=0.332
The Exome Aggregation ConsortiumOtherSub856C=0.680T=0.320
The Genome Aggregation DatabaseAfricanSub8694C=0.715T=0.285
The Genome Aggregation DatabaseAmericanSub834C=0.440T=0.560
The Genome Aggregation DatabaseEast AsianSub1614C=0.566T=0.434
The Genome Aggregation DatabaseEuropeSub18414C=0.760T=0.239
The Genome Aggregation DatabaseGlobalStudy-wide29858C=0.727T=0.272
The Genome Aggregation DatabaseOtherSub302C=0.740T=0.260
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.727T=0.272
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.777T=0.223
PMID Title Author Journal
20700436Multiple independent loci at chromosome 15q25.1 affect smoking quantity: a meta-analysis and comparison with lung cancer and COPD.Saccone NLPLoS Genet
18519524Variants in nicotinic receptors and risk for nicotine dependence.Bierut LJAm J Psychiatry
21229299Chromosome 15q24-25.1 variants, diet, and lung cancer susceptibility in cigarette smokers.Sakoda LCCancer Causes Control
20808433Associations of variants in CHRNA5/A3/B4 gene cluster with smoking behaviors in a Korean population.Li MDPLoS One
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
23692359CHRNA5-A3-B4 genetic variants alter nicotine intake and interact with tobacco use to influence body weight in Alaska Native tobacco users.Zhu AZAddiction
21606948Varenicline for smoking cessation: nausea severity and variation in nicotinic receptor genes.Swan GEPharmacogenomics J
23358500Variation in the alpha 5 nicotinic acetylcholine receptor subunit gene predicts cigarette smoking intensity as a function of nicotine content.Macqueen DAPharmacogenomics J
25036316Joint association of nicotinic acetylcholine receptor variants with abdominal obesity in American Indians: the Strong Heart Family Study.Zhu YPLoS One
19436041Human neuronal acetylcholine receptor A5-A3-B4 haplotypes are associated with multiple nicotine dependence phenotypes.Baker TBNicotine Tob Res
27166759Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions.Yang JMol Psychiatry
18414406Genetic variation in the CHRNA5 gene affects mRNA levels and is associated with risk for alcohol dependence.Wang JCMol Psychiatry
20736995Resequencing of nicotinic acetylcholine receptor genes and association of common and rare variants with the Fagerstrom test for nicotine dependence.Wessel JNeuropsychopharmacology
19443489Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in CHRNA5.Wang JCHum Mol Genet
26695521Mendelian Randomization - the Key to Understanding Aspects of Parkinson's Disease Causation?Noyce AJMov Disord
18618000A candidate gene approach identifies the CHRNA5-A3-B4 region as a risk factor for age-dependent nicotine addiction.Weiss RBPLoS Genet
21228559An exploratory study on the CHRNA3-CHRNA5-CHRNB4 cluster, smoking, and Parkinson's disease.Gao JNeurodegener Dis
19029397Nicotinic receptor gene variants influence susceptibility to heavy smoking.Stevens VLCancer Epidemiol Biomarkers Prev
20700147Nicotinic alpha5 receptor subunit mRNA expression is associated with distant 5' upstream polymorphisms.Smith RMEur J Hum Genet
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
rs5692070.001Drug response to nicotine18618000

eQTL of rs569207 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:78873119CHRNA5ENSG00000169684.9C>T1.9380e-1215257Putamen_basal_ganglia

meQTL of rs569207 in Fetal Brain

Probe ID Position Gene beta p-value
cg24631222chr15:78858424CHRNA50.02798232301940764.5607e-11

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 )
chr157883465278834702E067-38417
chr157883465278834702E069-38417
chr157883485878834908E069-38211
chr157883506878835124E069-37995
chr157883512578835267E069-37852
chr157883541478835508E069-37611
chr157883557978835628E069-37491
chr157883465278834702E070-38417
chr157885686878857013E072-16106
chr157883465278834702E073-38417
chr157883465278834702E081-38417
chr157883485878834908E081-38211
chr157883465278834702E082-38417
chr157883485878834908E082-38211
chr157886578678866130E082-6989
chr157891955378919674E08246434
chr157891979978919961E08246680







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr157883216578832234E067-40885
chr157883228778834159E067-38960
chr157885705278859300E067-13819
chr157883216578832234E068-40885
chr157883228778834159E068-38960
chr157891174978913845E06838630
chr157883216578832234E069-40885
chr157883228778834159E069-38960
chr157885705278859300E069-13819
chr157883216578832234E070-40885
chr157883228778834159E070-38960
chr157885705278859300E070-13819
chr157883216578832234E071-40885
chr157883228778834159E071-38960
chr157883216578832234E072-40885
chr157883228778834159E072-38960
chr157885705278859300E072-13819
chr157883216578832234E073-40885
chr157883228778834159E073-38960
chr157885705278859300E073-13819
chr157883216578832234E074-40885
chr157883228778834159E074-38960
chr157885705278859300E074-13819
chr157883228778834159E081-38960
chr157885705278859300E081-13819
chr157883216578832234E082-40885
chr157883228778834159E082-38960
chr157885705278859300E082-13819
chr157891174978913845E08238630