rs1880046

Homo sapiens
C>T
CTNNA3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0426 (12753/29900,GnomAD)
T=0418 (12191/29118,TOPMED)
T=0340 (1701/5008,1000G)
T=0450 (1736/3854,ALSPAC)
T=0457 (1693/3708,TWINSUK)
chr10:66878053 (GRCh38.p7) (10q21.3)
ND
GWASdb2
1   publication(s)
See rs on genome
19 Enhancers around
49 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.66878053C>T
GRCh37.p13 chr 10NC_000010.10:g.68637811C>T
CTNNA3 RefSeqGeneNG_034072.1:g.823139G>A

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
1000GenomesAfricanSub1322C=0.573T=0.427
1000GenomesAmericanSub694C=0.630T=0.370
1000GenomesEast AsianSub1008C=0.881T=0.119
1000GenomesEuropeSub1006C=0.569T=0.431
1000GenomesGlobalStudy-wide5008C=0.660T=0.340
1000GenomesSouth AsianSub978C=0.670T=0.330
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.550T=0.450
The Genome Aggregation DatabaseAfricanSub8716C=0.582T=0.418
The Genome Aggregation DatabaseAmericanSub836C=0.710T=0.290
The Genome Aggregation DatabaseEast AsianSub1602C=0.861T=0.139
The Genome Aggregation DatabaseEuropeSub18444C=0.538T=0.461
The Genome Aggregation DatabaseGlobalStudy-wide29900C=0.573T=0.426
The Genome Aggregation DatabaseOtherSub302C=0.570T=0.430
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.581T=0.418
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.543T=0.457
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs18800460.000502nicotine dependence17158188

eQTL of rs1880046 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 rs1880046 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 )
chr106859783768598117E067-39694
chr106859701368597217E070-40594
chr106859723368597386E070-40425
chr106859740968597538E070-40273
chr106859758868597779E070-40032
chr106865193168652035E07014120
chr106865236468652418E07014553
chr106865249368652925E07014682
chr106865295768653174E07015146
chr106865341068653473E07015599
chr106865348468653645E07015673
chr106865405068654090E07016239
chr106860923868609347E071-28464
chr106860938368609549E071-28262
chr106860409268604245E074-33566
chr106860629568606345E081-31466
chr106862494468624994E081-12817
chr106862518968625260E081-12551
chr106865295768653174E08115146





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr106868503068686378E06747219
chr106868642868686495E06748617
chr106868670068686822E06748889
chr106868683968686889E06749028
chr106868707068687221E06749259
chr106868503068686378E06847219
chr106868642868686495E06848617
chr106868670068686822E06848889
chr106868683968686889E06849028
chr106868707068687221E06849259
chr106868503068686378E06947219
chr106868642868686495E06948617
chr106868670068686822E06948889
chr106868683968686889E06949028
chr106868707068687221E06949259
chr106868503068686378E07047219
chr106868642868686495E07048617
chr106868670068686822E07048889
chr106868683968686889E07049028
chr106868707068687221E07049259
chr106868503068686378E07147219
chr106868642868686495E07148617
chr106868670068686822E07148889
chr106868683968686889E07149028
chr106868707068687221E07149259
chr106868503068686378E07247219
chr106868642868686495E07248617
chr106868670068686822E07248889
chr106868683968686889E07249028
chr106868707068687221E07249259
chr106868503068686378E07347219
chr106868642868686495E07348617
chr106868670068686822E07348889
chr106868683968686889E07349028
chr106868707068687221E07349259
chr106868503068686378E07447219
chr106868642868686495E07448617
chr106868670068686822E07448889
chr106868683968686889E07449028
chr106868707068687221E07449259
chr106868503068686378E08147219
chr106868642868686495E08148617
chr106868670068686822E08148889
chr106868683968686889E08149028
chr106868503068686378E08247219
chr106868642868686495E08248617
chr106868670068686822E08248889
chr106868683968686889E08249028
chr106868707068687221E08249259