rs6487980

Homo sapiens
T>C
OVOS2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0122 (3666/29944,GnomAD)
C=0177 (5181/29118,TOPMED)
C=0140 (701/5008,1000G)
C=0058 (223/3854,ALSPAC)
C=0056 (206/3708,TWINSUK)
chr12:31157874 (GRCh38.p7) (12p11.21)
AD
GWASdb2
1   publication(s)
See rs on genome
2 Enhancers around
36 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.31157874T>C
GRCh37.p13 chr 12NC_000012.11:g.31310808T>C
GRCh38.p7 chr 12 alt locus HSCHR12_4_CTG2NT_187587.1:g.48668T>C

Gene: OVOS2, uncharacterized OVOS2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
OVOS2 transcriptXM_017020288.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.714C=0.286
1000GenomesAmericanSub694T=0.900C=0.100
1000GenomesEast AsianSub1008T=0.886C=0.114
1000GenomesEuropeSub1006T=0.939C=0.061
1000GenomesGlobalStudy-wide5008T=0.860C=0.140
1000GenomesSouth AsianSub978T=0.920C=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.942C=0.058
The Genome Aggregation DatabaseAfricanSub8698T=0.723C=0.277
The Genome Aggregation DatabaseAmericanSub838T=0.920C=0.080
The Genome Aggregation DatabaseEast AsianSub1622T=0.883C=0.117
The Genome Aggregation DatabaseEuropeSub18484T=0.947C=0.052
The Genome Aggregation DatabaseGlobalStudy-wide29944T=0.877C=0.122
The Genome Aggregation DatabaseOtherSub302T=0.870C=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.822C=0.177
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.944C=0.056
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
rs64879800.00055alcohol dependence(early age of onset)20201924
rs64879800.0009alcohol dependence20201924

eQTL of rs6487980 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 rs6487980 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 )
chr123132821031328262E07017402
chr123126982531269879E071-40929


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr123127099731272685E067-38123
chr123127280031273000E067-37808
chr123127099731272685E068-38123
chr123127280031273000E068-37808
chr123127302231273191E068-37617
chr123127326731273361E068-37447
chr123127280031273000E069-37808
chr123127302231273191E069-37617
chr123127326731273361E069-37447
chr123126995431270689E070-40119
chr123127076031270967E070-39841
chr123127099731272685E070-38123
chr123127280031273000E070-37808
chr123127302231273191E070-37617
chr123127326731273361E070-37447
chr123127358831273652E070-37156
chr123127369231273964E070-36844
chr123127302231273191E071-37617
chr123127326731273361E071-37447
chr123127358831273652E071-37156
chr123127280031273000E072-37808
chr123127302231273191E072-37617
chr123127326731273361E072-37447
chr123127302231273191E073-37617
chr123127326731273361E073-37447
chr123127358831273652E073-37156
chr123127099731272685E074-38123
chr123127280031273000E074-37808
chr123127302231273191E074-37617
chr123127326731273361E074-37447
chr123126995431270689E082-40119
chr123127076031270967E082-39841
chr123127099731272685E082-38123
chr123127280031273000E082-37808
chr123127302231273191E082-37617
chr123127326731273361E082-37447