rs9332406

Homo sapiens
C>A
CTNNA3 : Intron Variant
LOC101928961 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0299 (8954/29946,GnomAD)
A=0276 (8063/29118,TOPMED)
A=0338 (1692/5008,1000G)
A=0370 (1426/3854,ALSPAC)
A=0376 (1395/3708,TWINSUK)
chr10:66910441 (GRCh38.p7) (10q21.3)
ND
GWASdb2
2   publication(s)
See rs on genome
151 Enhancers around
111 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.66910441C>A
GRCh37.p13 chr 10NC_000010.10:g.68670199C>A
CTNNA3 RefSeqGeneNG_034072.1:g.790751G>T

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

Gene: LOC101928961, uncharacterized LOC101928961(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC101928961 transcriptNR_111911.1:n.277...NR_111911.1:n.2770G>TG>TNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.937A=0.063
1000GenomesAmericanSub694C=0.580A=0.420
1000GenomesEast AsianSub1008C=0.509A=0.491
1000GenomesEuropeSub1006C=0.624A=0.376
1000GenomesGlobalStudy-wide5008C=0.662A=0.338
1000GenomesSouth AsianSub978C=0.550A=0.450
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.630A=0.370
The Genome Aggregation DatabaseAfricanSub8722C=0.889A=0.111
The Genome Aggregation DatabaseAmericanSub838C=0.530A=0.470
The Genome Aggregation DatabaseEast AsianSub1614C=0.514A=0.486
The Genome Aggregation DatabaseEuropeSub18470C=0.639A=0.360
The Genome Aggregation DatabaseGlobalStudy-wide29946C=0.701A=0.299
The Genome Aggregation DatabaseOtherSub302C=0.520A=0.480
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.723A=0.276
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.624A=0.376
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet
14740319Matching strategies for genetic association studies in structured populations.Hinds DAAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs93324069.71E-05nicotine dependence17158188

eQTL of rs9332406 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 rs9332406 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 )
chr106869982268699872E06729623
chr106870011668700192E06729917
chr106870036368700447E06730164
chr106870057268700750E06730373
chr106870085168701071E06730652
chr106870164168701933E06731442
chr106870268468702781E06732485
chr106870625468706355E06736055
chr106870656268706652E06736363
chr106871162468711689E06741425
chr106871170268712046E06741503
chr106871633968716419E06746140
chr106871650668716657E06746307
chr106871754668717645E06747347
chr106871765268717702E06747453
chr106871776268717863E06747563
chr106871788268717926E06747683
chr106871795868718034E06747759
chr106871809068719347E06747891
chr106870011668700192E06829917
chr106870036368700447E06830164
chr106870057268700750E06830373
chr106870085168701071E06830652
chr106870164168701933E06831442
chr106870950168709545E06839302
chr106871162468711689E06841425
chr106871170268712046E06841503
chr106871217568712236E06841976
chr106871633968716419E06846140
chr106871650668716657E06846307
chr106871754668717645E06847347
chr106871765268717702E06847453
chr106871776268717863E06847563
chr106871788268717926E06847683
chr106871795868718034E06847759
chr106871809068719347E06847891
chr106869289468692944E06922695
chr106869969168699731E06929492
chr106869982268699872E06929623
chr106870011668700192E06929917
chr106870036368700447E06930164
chr106870057268700750E06930373
chr106870085168701071E06930652
chr106870135368701554E06931154
chr106870164168701933E06931442
chr106870950168709545E06939302
chr106871162468711689E06941425
chr106871170268712046E06941503
chr106871217568712236E06941976
chr106871633968716419E06946140
chr106871650668716657E06946307
chr106871754668717645E06947347
chr106871765268717702E06947453
chr106871776268717863E06947563
chr106871788268717926E06947683
chr106871795868718034E06947759
chr106871809068719347E06947891
chr106871960368719729E06949404
chr106865193168652035E070-18164
chr106865236468652418E070-17781
chr106865249368652925E070-17274
chr106865295768653174E070-17025
chr106865341068653473E070-16726
chr106865348468653645E070-16554
chr106865405068654090E070-16109
chr106870085168701071E07030652
chr106870135368701554E07031154
chr106870164168701933E07031442
chr106871162468711689E07041425
chr106871170268712046E07041503
chr106871754668717645E07047347
chr106871765268717702E07047453
chr106871776268717863E07047563
chr106871788268717926E07047683
chr106871795868718034E07047759
chr106871809068719347E07047891
chr106869289468692944E07122695
chr106869320568693268E07123006
chr106869969168699731E07129492
chr106869982268699872E07129623
chr106870011668700192E07129917
chr106870036368700447E07130164
chr106870057268700750E07130373
chr106870085168701071E07130652
chr106870164168701933E07131442
chr106871162468711689E07141425
chr106871170268712046E07141503
chr106871217568712236E07141976
chr106871633968716419E07146140
chr106871650668716657E07146307
chr106871754668717645E07147347
chr106871765268717702E07147453
chr106871776268717863E07147563
chr106871788268717926E07147683
chr106871795868718034E07147759
chr106871809068719347E07147891
chr106869289468692944E07222695
chr106869320568693268E07223006
chr106869982268699872E07229623
chr106870011668700192E07229917
chr106870036368700447E07230164
chr106870057268700750E07230373
chr106871162468711689E07241425
chr106871170268712046E07241503
chr106871217568712236E07241976
chr106871633968716419E07246140
chr106871650668716657E07246307
chr106871754668717645E07247347
chr106871765268717702E07247453
chr106871776268717863E07247563
chr106871788268717926E07247683
chr106871795868718034E07247759
chr106871809068719347E07247891
chr106869372468693811E07323525
chr106869457868694642E07324379
chr106869468168694753E07324482
chr106870036368700447E07330164
chr106870057268700750E07330373
chr106870950168709545E07339302
chr106870963768709763E07339438
chr106871633968716419E07346140
chr106871650668716657E07346307
chr106871754668717645E07347347
chr106871765268717702E07347453
chr106871776268717863E07347563
chr106871788268717926E07347683
chr106871795868718034E07347759
chr106871809068719347E07347891
chr106869289468692944E07422695
chr106869320568693268E07423006
chr106869969168699731E07429492
chr106869982268699872E07429623
chr106870135368701554E07431154
chr106871162468711689E07441425
chr106871170268712046E07441503
chr106871217568712236E07441976
chr106871242568712475E07442226
chr106871548668715565E07445287
chr106871633968716419E07446140
chr106871809068719347E07447891
chr106862494468624994E081-45205
chr106862518968625260E081-44939
chr106865295768653174E081-17025
chr106869982268699872E08129623
chr106870011668700192E08129917
chr106870036368700447E08130164
chr106870057268700750E08130373
chr106870085168701071E08130652
chr106870135368701554E08131154
chr106870164168701933E08131442
chr106870057268700750E08230373










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr106868503068686378E06714831
chr106868642868686495E06716229
chr106868670068686822E06716501
chr106868683968686889E06716640
chr106868707068687221E06716871
chr106868730968689320E06717110
chr106868934968689639E06719150
chr106869088568690947E06720686
chr106869103768691393E06720838
chr106869151968691618E06721320
chr106869163368691687E06721434
chr106869174468692004E06721545
chr106869217668692226E06721977
chr106868503068686378E06814831
chr106868642868686495E06816229
chr106868670068686822E06816501
chr106868683968686889E06816640
chr106868707068687221E06816871
chr106868730968689320E06817110
chr106868934968689639E06819150
chr106869088568690947E06820686
chr106869103768691393E06820838
chr106869151968691618E06821320
chr106869163368691687E06821434
chr106869174468692004E06821545
chr106869217668692226E06821977
chr106868503068686378E06914831
chr106868642868686495E06916229
chr106868670068686822E06916501
chr106868683968686889E06916640
chr106868707068687221E06916871
chr106868730968689320E06917110
chr106868934968689639E06919150
chr106869151968691618E06921320
chr106869163368691687E06921434
chr106869174468692004E06921545
chr106869217668692226E06921977
chr106868503068686378E07014831
chr106868642868686495E07016229
chr106868670068686822E07016501
chr106868683968686889E07016640
chr106868707068687221E07016871
chr106868730968689320E07017110
chr106868934968689639E07019150
chr106869151968691618E07021320
chr106869163368691687E07021434
chr106869174468692004E07021545
chr106868503068686378E07114831
chr106868642868686495E07116229
chr106868670068686822E07116501
chr106868683968686889E07116640
chr106868707068687221E07116871
chr106868730968689320E07117110
chr106868934968689639E07119150
chr106869088568690947E07120686
chr106869103768691393E07120838
chr106869151968691618E07121320
chr106869163368691687E07121434
chr106869174468692004E07121545
chr106869217668692226E07121977
chr106868503068686378E07214831
chr106868642868686495E07216229
chr106868670068686822E07216501
chr106868683968686889E07216640
chr106868707068687221E07216871
chr106868730968689320E07217110
chr106868934968689639E07219150
chr106869088568690947E07220686
chr106869103768691393E07220838
chr106869151968691618E07221320
chr106869163368691687E07221434
chr106869174468692004E07221545
chr106869217668692226E07221977
chr106868503068686378E07314831
chr106868642868686495E07316229
chr106868670068686822E07316501
chr106868683968686889E07316640
chr106868707068687221E07316871
chr106868730968689320E07317110
chr106868934968689639E07319150
chr106869088568690947E07320686
chr106869103768691393E07320838
chr106869151968691618E07321320
chr106869163368691687E07321434
chr106869174468692004E07321545
chr106869217668692226E07321977
chr106868503068686378E07414831
chr106868642868686495E07416229
chr106868670068686822E07416501
chr106868683968686889E07416640
chr106868707068687221E07416871
chr106868730968689320E07417110
chr106868503068686378E08114831
chr106868642868686495E08116229
chr106868670068686822E08116501
chr106868683968686889E08116640
chr106868730968689320E08117110
chr106868934968689639E08119150
chr106869103768691393E08120838
chr106868503068686378E08214831
chr106868642868686495E08216229
chr106868670068686822E08216501
chr106868683968686889E08216640
chr106868707068687221E08216871
chr106868730968689320E08217110
chr106868934968689639E08219150
chr106869088568690947E08220686
chr106869103768691393E08220838
chr106869151968691618E08221320
chr106869163368691687E08221434
chr106869174468692004E08221545