rs13404879

Homo sapiens
G>T
CAB39 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0212 (6321/29762,GnomAD)
T=0297 (8655/29118,TOPMED)
T=0225 (1129/5008,1000G)
T=0074 (285/3854,ALSPAC)
T=0085 (317/3708,TWINSUK)
chr2:230723394 (GRCh38.p7) (2q37.1)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.230723394G>T
GRCh37.p13 chr 2NC_000002.11:g.231588109G>T

Gene: CAB39, calcium binding protein 39(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CAB39 transcript variant 2NM_001130849.1:c.N/AIntron Variant
CAB39 transcript variant 3NM_001130850.1:c.N/AIntron Variant
CAB39 transcript variant 1NM_016289.3:c.N/AIntron Variant
CAB39 transcript variant X1XM_011511350.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.365T=0.635
1000GenomesAmericanSub694G=0.890T=0.110
1000GenomesEast AsianSub1008G=0.933T=0.067
1000GenomesEuropeSub1006G=0.920T=0.080
1000GenomesGlobalStudy-wide5008G=0.775T=0.225
1000GenomesSouth AsianSub978G=0.930T=0.070
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.926T=0.074
The Genome Aggregation DatabaseAfricanSub8664G=0.449T=0.551
The Genome Aggregation DatabaseAmericanSub836G=0.920T=0.080
The Genome Aggregation DatabaseEast AsianSub1620G=0.975T=0.025
The Genome Aggregation DatabaseEuropeSub18342G=0.923T=0.076
The Genome Aggregation DatabaseGlobalStudy-wide29762G=0.787T=0.212
The Genome Aggregation DatabaseOtherSub300G=0.880T=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.702T=0.297
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.915T=0.085
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs134048790.00095alcohol dependence20201924

eQTL of rs13404879 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 rs13404879 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 )
chr2231580545231580595E067-7514
chr2231582211231582261E067-5848
chr2231582286231582469E067-5640
chr2231582481231582658E067-5451
chr2231582802231583082E067-5027
chr2231584571231584661E067-3448
chr2231584774231584855E067-3254
chr2231602916231603530E06714807
chr2231623947231624121E06735838
chr2231580545231580595E068-7514
chr2231582211231582261E068-5848
chr2231582286231582469E068-5640
chr2231582481231582658E068-5451
chr2231600670231600765E06812561
chr2231602195231602249E06814086
chr2231602514231602906E06814405
chr2231602916231603530E06814807
chr2231615732231616286E06827623
chr2231623947231624121E06835838
chr2231624214231624407E06836105
chr2231555331231555518E069-32591
chr2231580545231580595E069-7514
chr2231582286231582469E069-5640
chr2231582481231582658E069-5451
chr2231582802231583082E069-5027
chr2231602916231603530E06914807
chr2231615732231616286E06927623
chr2231623345231623504E06935236
chr2231623512231623891E06935403
chr2231623947231624121E06935838
chr2231624214231624407E06936105
chr2231580545231580595E070-7514
chr2231623947231624121E07035838
chr2231580805231580875E071-7234
chr2231582211231582261E071-5848
chr2231582286231582469E071-5640
chr2231582481231582658E071-5451
chr2231582802231583082E071-5027
chr2231602916231603530E07114807
chr2231615732231616286E07127623
chr2231616417231616469E07128308
chr2231621875231621956E07133766
chr2231622073231622215E07133964
chr2231622270231622438E07134161
chr2231629960231630061E07141851
chr2231580545231580595E072-7514
chr2231580805231580875E072-7234
chr2231582286231582469E072-5640
chr2231582481231582658E072-5451
chr2231582802231583082E072-5027
chr2231602916231603530E07214807
chr2231615732231616286E07227623
chr2231620627231621187E07232518
chr2231623512231623891E07235403
chr2231623947231624121E07235838
chr2231630275231630623E07242166
chr2231555760231556208E073-31901
chr2231580545231580595E073-7514
chr2231582211231582261E073-5848
chr2231582286231582469E073-5640
chr2231582481231582658E073-5451
chr2231617518231617727E07329409
chr2231623345231623504E07335236
chr2231623512231623891E07335403
chr2231623947231624121E07335838
chr2231624214231624407E07336105
chr2231580545231580595E074-7514
chr2231582286231582469E074-5640
chr2231582481231582658E074-5451
chr2231582802231583082E074-5027
chr2231584571231584661E074-3448
chr2231584774231584855E074-3254
chr2231602514231602906E07414405
chr2231602916231603530E07414807
chr2231615732231616286E07427623
chr2231623345231623504E07435236
chr2231623512231623891E07435403
chr2231623947231624121E07435838
chr2231555331231555518E081-32591
chr2231580545231580595E081-7514
chr2231555331231555518E082-32591










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2231576818231579281E067-8828
chr2231576818231579281E068-8828
chr2231576818231579281E069-8828
chr2231576818231579281E070-8828
chr2231576818231579281E071-8828
chr2231576818231579281E072-8828
chr2231576818231579281E073-8828
chr2231576818231579281E074-8828
chr2231576818231579281E081-8828
chr2231576818231579281E082-8828