rs7179733

Homo sapiens
C>T
CHRNA7 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0439 (13128/29852,GnomAD)
T=0393 (11455/29118,TOPMED)
T=0371 (1856/5008,1000G)
C==0409 (1577/3854,ALSPAC)
C==0421 (1562/3708,TWINSUK)
chr15:32081490 (GRCh38.p7) (15q13.3)
AD
GWASdb2
2   publication(s)
See rs on genome
36 Enhancers around
4 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.32081490C>T
GRCh37.p13 chr 15NC_000015.9:g.32373693C>T
CHRNA7 RefSeqGeneNG_009216.1:g.55968C>T
GRCh38.p7 chr 15 fix patch HG2139_PATCHNW_011332701.1:g.4254161T>C
GRCh38.p7 chr 15 alt locus HSCHR15_4_CTG8NT_187660.1:g.4366613T>C

Gene: CHRNA7, cholinergic receptor nicotinic alpha 7 subunit(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CHRNA7 transcript variant 1NM_000746.5:c.N/AIntron Variant
CHRNA7 transcript variant 2NM_001190455.2:c.N/AIntron Variant
CHRNA7 transcript variant 3NR_046324.1:n.N/AIntron Variant
CHRNA7 transcript variant X5XM_011521178.2:c.N/AIntron Variant
CHRNA7 transcript variant X2XM_017021882.1:c.N/AIntron Variant
CHRNA7 transcript variant X3XM_017021883.1:c.N/AIntron Variant
CHRNA7 transcript variant X6XM_017021884.1:c.N/AIntron Variant
CHRNA7 transcript variant X1XM_011521176.2:c.N/AGenic Upstream Transcript Variant
CHRNA7 transcript variant X4XM_011521177.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.877T=0.123
1000GenomesAmericanSub694C=0.600T=0.400
1000GenomesEast AsianSub1008C=0.811T=0.189
1000GenomesEuropeSub1006C=0.417T=0.583
1000GenomesGlobalStudy-wide5008C=0.629T=0.371
1000GenomesSouth AsianSub978C=0.340T=0.660
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.409T=0.591
The Genome Aggregation DatabaseAfricanSub8690C=0.807T=0.193
The Genome Aggregation DatabaseAmericanSub834C=0.580T=0.420
The Genome Aggregation DatabaseEast AsianSub1606C=0.824T=0.176
The Genome Aggregation DatabaseEuropeSub18420C=0.422T=0.577
The Genome Aggregation DatabaseGlobalStudy-wide29852C=0.560T=0.439
The Genome Aggregation DatabaseOtherSub302C=0.400T=0.600
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.606T=0.393
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.421T=0.579
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
17373692No evidence for association between 19 cholinergic genes and bipolar disorder.Shi JAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs71797330.00034alcohol dependence20201924

eQTL of rs7179733 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs7179733 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 )
chr153232525232325962E070-47731
chr153238890132388995E07015208
chr153238950232389746E07015809
chr153239078932391004E07017096
chr153239152332391842E07017830
chr153239191732392021E07018224
chr153239212132392165E07018428
chr153239220132392480E07018508
chr153239267532392785E07018982
chr153239287432392943E07019181
chr153239333032393440E07019637
chr153232525232325962E074-47731
chr153238910932389449E08115416
chr153238950232389746E08115809
chr153238999732390071E08116304
chr153239007332390176E08116380
chr153239021932390696E08116526
chr153239078932391004E08117096
chr153239152332391842E08117830
chr153239191732392021E08118224
chr153239212132392165E08118428
chr153239220132392480E08118508
chr153239267532392785E08118982
chr153239287432392943E08119181
chr153241493232415083E08141239
chr153241529232415416E08141599
chr153242199732422294E08148304
chr153238999732390071E08216304
chr153239007332390176E08216380
chr153239021932390696E08216526
chr153239078932391004E08217096
chr153239152332391842E08217830
chr153239191732392021E08218224
chr153239212132392165E08218428
chr153239220132392480E08218508
chr153239267532392785E08218982




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr153232376332323832E070-49861
chr153232376332323832E072-49861
chr153232386132323968E072-49725
chr153232376332323832E082-49861