rs4142041

Homo sapiens
A>G
CTNNA3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0302 (9050/29920,GnomAD)
G=0278 (8103/29118,TOPMED)
G=0356 (1784/5008,1000G)
G=0373 (1437/3854,ALSPAC)
G=0375 (1392/3708,TWINSUK)
chr10:66881193 (GRCh38.p7) (10q21.3)
ND
GWASdb2 | GWASCatalog
3   publication(s)
See rs on genome
19 Enhancers around
74 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.66881193A>G
GRCh37.p13 chr 10NC_000010.10:g.68640951A>G
CTNNA3 RefSeqGeneNG_034072.1:g.819999T>C

Gene: CTNNA3, catenin alpha 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CTNNA3 transcript variant 2NM_001127384.2:c.N/AIntron Variant
CTNNA3 transcript variant 1NM_013266.3:c.N/AIntron Variant
CTNNA3 transcript variant 3NM_001291133.1:c.N/AGenic Downstream Transcript Variant
CTNNA3 transcript variant X1XM_017016151.1:c.N/AIntron Variant
CTNNA3 transcript variant X2XM_017016152.1:c.N/AIntron Variant
CTNNA3 transcript variant X3XM_017016153.1:c.N/AIntron Variant
CTNNA3 transcript variant X4XM_017016154.1:c.N/AIntron Variant
CTNNA3 transcript variant X5XM_017016155.1:c.N/AIntron Variant
CTNNA3 transcript variant X6XM_017016156.1:c.N/AIntron Variant
CTNNA3 transcript variant X7XM_017016157.1:c.N/AGenic Upstream Transcript Variant
CTNNA3 transcript variant X8XM_017016158.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.943G=0.057
1000GenomesAmericanSub694A=0.550G=0.450
1000GenomesEast AsianSub1008A=0.481G=0.519
1000GenomesEuropeSub1006A=0.618G=0.382
1000GenomesGlobalStudy-wide5008A=0.644G=0.356
1000GenomesSouth AsianSub978A=0.500G=0.500
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.627G=0.373
The Genome Aggregation DatabaseAfricanSub8730A=0.895G=0.105
The Genome Aggregation DatabaseAmericanSub836A=0.460G=0.540
The Genome Aggregation DatabaseEast AsianSub1590A=0.487G=0.513
The Genome Aggregation DatabaseEuropeSub18464A=0.635G=0.364
The Genome Aggregation DatabaseGlobalStudy-wide29920A=0.697G=0.302
The Genome Aggregation DatabaseOtherSub300A=0.510G=0.490
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.721G=0.278
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.625G=0.375
PMID Title Author Journal
18565990Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence.Saccone SFBioinformatics
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet
18783506Association of a single nucleotide polymorphism in neuronal acetylcholine receptor subunit alpha 5 (CHRNA5) with smoking status and with 'pleasurable buzz' during early experimentation with smoking.Sherva RAddiction

P-Value

SNP ID p-value Traits Study
rs41420416E-06nicotine dependence17158188

eQTL of rs4142041 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 rs4142041 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 )
chr106859783768598117E067-42834
chr106859701368597217E070-43734
chr106859723368597386E070-43565
chr106859740968597538E070-43413
chr106859758868597779E070-43172
chr106865193168652035E07010980
chr106865236468652418E07011413
chr106865249368652925E07011542
chr106865295768653174E07012006
chr106865341068653473E07012459
chr106865348468653645E07012533
chr106865405068654090E07013099
chr106860923868609347E071-31604
chr106860938368609549E071-31402
chr106860409268604245E074-36706
chr106860629568606345E081-34606
chr106862494468624994E081-15957
chr106862518968625260E081-15691
chr106865295768653174E08112006





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr106868503068686378E06744079
chr106868642868686495E06745477
chr106868670068686822E06745749
chr106868683968686889E06745888
chr106868707068687221E06746119
chr106868730968689320E06746358
chr106868934968689639E06748398
chr106869088568690947E06749934
chr106868503068686378E06844079
chr106868642868686495E06845477
chr106868670068686822E06845749
chr106868683968686889E06845888
chr106868707068687221E06846119
chr106868730968689320E06846358
chr106868934968689639E06848398
chr106869088568690947E06849934
chr106868503068686378E06944079
chr106868642868686495E06945477
chr106868670068686822E06945749
chr106868683968686889E06945888
chr106868707068687221E06946119
chr106868730968689320E06946358
chr106868934968689639E06948398
chr106868503068686378E07044079
chr106868642868686495E07045477
chr106868670068686822E07045749
chr106868683968686889E07045888
chr106868707068687221E07046119
chr106868730968689320E07046358
chr106868934968689639E07048398
chr106868503068686378E07144079
chr106868642868686495E07145477
chr106868670068686822E07145749
chr106868683968686889E07145888
chr106868707068687221E07146119
chr106868730968689320E07146358
chr106868934968689639E07148398
chr106869088568690947E07149934
chr106868503068686378E07244079
chr106868642868686495E07245477
chr106868670068686822E07245749
chr106868683968686889E07245888
chr106868707068687221E07246119
chr106868730968689320E07246358
chr106868934968689639E07248398
chr106869088568690947E07249934
chr106868503068686378E07344079
chr106868642868686495E07345477
chr106868670068686822E07345749
chr106868683968686889E07345888
chr106868707068687221E07346119
chr106868730968689320E07346358
chr106868934968689639E07348398
chr106869088568690947E07349934
chr106868503068686378E07444079
chr106868642868686495E07445477
chr106868670068686822E07445749
chr106868683968686889E07445888
chr106868707068687221E07446119
chr106868730968689320E07446358
chr106868503068686378E08144079
chr106868642868686495E08145477
chr106868670068686822E08145749
chr106868683968686889E08145888
chr106868730968689320E08146358
chr106868934968689639E08148398
chr106868503068686378E08244079
chr106868642868686495E08245477
chr106868670068686822E08245749
chr106868683968686889E08245888
chr106868707068687221E08246119
chr106868730968689320E08246358
chr106868934968689639E08248398
chr106869088568690947E08249934