rs6717266

Homo sapiens
G>A
CAB39 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0139 (4188/29930,GnomAD)
A=0184 (5368/29118,TOPMED)
A=0155 (774/5008,1000G)
A=0074 (284/3854,ALSPAC)
A=0084 (311/3708,TWINSUK)
chr2:230748426 (GRCh38.p7) (2q37.1)
AD
GWASdb2
1   publication(s)
See rs on genome
101 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.230748426G>A
GRCh37.p13 chr 2NC_000002.11:g.231613141G>A

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=0.623A=0.377
1000GenomesAmericanSub694G=0.910A=0.090
1000GenomesEast AsianSub1008G=0.933A=0.067
1000GenomesEuropeSub1006G=0.920A=0.080
1000GenomesGlobalStudy-wide5008G=0.845A=0.155
1000GenomesSouth AsianSub978G=0.930A=0.070
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.926A=0.074
The Genome Aggregation DatabaseAfricanSub8704G=0.696A=0.304
The Genome Aggregation DatabaseAmericanSub838G=0.930A=0.070
The Genome Aggregation DatabaseEast AsianSub1620G=0.974A=0.026
The Genome Aggregation DatabaseEuropeSub18466G=0.924A=0.075
The Genome Aggregation DatabaseGlobalStudy-wide29930G=0.860A=0.139
The Genome Aggregation DatabaseOtherSub302G=0.880A=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.815A=0.184
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.916A=0.084
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
rs67172660.0003alcohol dependence(early age of onset)20201924
rs67172660.00037alcohol dependence20201924

eQTL of rs6717266 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 rs6717266 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 )
chr2231580545231580595E067-32546
chr2231582211231582261E067-30880
chr2231582286231582469E067-30672
chr2231582481231582658E067-30483
chr2231582802231583082E067-30059
chr2231584571231584661E067-28480
chr2231584774231584855E067-28286
chr2231602916231603530E067-9611
chr2231623947231624121E06710806
chr2231646016231646656E06732875
chr2231658439231659623E06745298
chr2231580545231580595E068-32546
chr2231582211231582261E068-30880
chr2231582286231582469E068-30672
chr2231582481231582658E068-30483
chr2231600670231600765E068-12376
chr2231602195231602249E068-10892
chr2231602514231602906E068-10235
chr2231602916231603530E068-9611
chr2231615732231616286E0682591
chr2231623947231624121E06810806
chr2231624214231624407E06811073
chr2231642969231643107E06829828
chr2231643430231643580E06830289
chr2231645875231645935E06832734
chr2231646016231646656E06832875
chr2231646661231646717E06833520
chr2231649498231650014E06836357
chr2231650166231650351E06837025
chr2231580545231580595E069-32546
chr2231582286231582469E069-30672
chr2231582481231582658E069-30483
chr2231582802231583082E069-30059
chr2231602916231603530E069-9611
chr2231615732231616286E0692591
chr2231623345231623504E06910204
chr2231623512231623891E06910371
chr2231623947231624121E06910806
chr2231624214231624407E06911073
chr2231646016231646656E06932875
chr2231646661231646717E06933520
chr2231580545231580595E070-32546
chr2231623947231624121E07010806
chr2231580805231580875E071-32266
chr2231582211231582261E071-30880
chr2231582286231582469E071-30672
chr2231582481231582658E071-30483
chr2231582802231583082E071-30059
chr2231602916231603530E071-9611
chr2231615732231616286E0712591
chr2231616417231616469E0713276
chr2231621875231621956E0718734
chr2231622073231622215E0718932
chr2231622270231622438E0719129
chr2231629960231630061E07116819
chr2231646016231646656E07132875
chr2231646661231646717E07133520
chr2231658439231659623E07145298
chr2231661131231661202E07147990
chr2231661247231661453E07148106
chr2231662208231662282E07149067
chr2231662519231662833E07149378
chr2231580545231580595E072-32546
chr2231580805231580875E072-32266
chr2231582286231582469E072-30672
chr2231582481231582658E072-30483
chr2231582802231583082E072-30059
chr2231602916231603530E072-9611
chr2231615732231616286E0722591
chr2231620627231621187E0727486
chr2231623512231623891E07210371
chr2231623947231624121E07210806
chr2231630275231630623E07217134
chr2231646016231646656E07232875
chr2231658439231659623E07245298
chr2231580545231580595E073-32546
chr2231582211231582261E073-30880
chr2231582286231582469E073-30672
chr2231582481231582658E073-30483
chr2231617518231617727E0734377
chr2231623345231623504E07310204
chr2231623512231623891E07310371
chr2231623947231624121E07310806
chr2231624214231624407E07311073
chr2231643430231643580E07330289
chr2231580545231580595E074-32546
chr2231582286231582469E074-30672
chr2231582481231582658E074-30483
chr2231582802231583082E074-30059
chr2231584571231584661E074-28480
chr2231584774231584855E074-28286
chr2231602514231602906E074-10235
chr2231602916231603530E074-9611
chr2231615732231616286E0742591
chr2231623345231623504E07410204
chr2231623512231623891E07410371
chr2231623947231624121E07410806
chr2231646016231646656E07432875
chr2231580545231580595E081-32546
chr2231658088231658173E08144947
chr2231658439231659623E08145298









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2231576818231579281E067-33860
chr2231576818231579281E068-33860
chr2231576818231579281E069-33860
chr2231576818231579281E070-33860
chr2231576818231579281E071-33860
chr2231576818231579281E072-33860
chr2231576818231579281E073-33860
chr2231576818231579281E074-33860
chr2231576818231579281E081-33860
chr2231576818231579281E082-33860