rs6039005

Homo sapiens
G>A / G>T
LOC105372520 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0335 (10018/29884,GnomAD)
T=0426 (12415/29118,TOPMED)
T=0441 (2207/5008,1000G)
T=0181 (699/3854,ALSPAC)
T=0195 (723/3708,TWINSUK)
chr20:8025549 (GRCh38.p7) (20p12.3)
AD
GWASdb2
1   publication(s)
See rs on genome
6 Enhancers around
17 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.8025549G>A
GRCh38.p7 chr 20NC_000020.11:g.8025549G>T
GRCh37.p13 chr 20NC_000020.10:g.8006196G>A
GRCh37.p13 chr 20NC_000020.10:g.8006196G>T

Gene: LOC105372520, uncharacterized LOC105372520(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105372520 transcript variant X2XR_001754487.1:n.N/AIntron Variant
LOC105372520 transcript variant X3XR_001754488.1:n.N/AIntron Variant
LOC105372520 transcript variant X4XR_937237.2:n.N/AIntron Variant
LOC105372520 transcript variant X5XR_937238.2:n.N/AIntron Variant
LOC105372520 transcript variant X1XR_937239.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.219T=0.781
1000GenomesAmericanSub694G=0.700T=0.300
1000GenomesEast AsianSub1008G=0.684T=0.316
1000GenomesEuropeSub1006G=0.792T=0.208
1000GenomesGlobalStudy-wide5008G=0.559T=0.441
1000GenomesSouth AsianSub978G=0.550T=0.450
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.819T=0.181
The Genome Aggregation DatabaseAfricanSub8694G=0.307A=0.000
The Genome Aggregation DatabaseAmericanSub832G=0.760A=0.00,
The Genome Aggregation DatabaseEast AsianSub1616G=0.700A=0.000
The Genome Aggregation DatabaseEuropeSub18444G=0.824A=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29884G=0.664A=0.000
The Genome Aggregation DatabaseOtherSub298G=0.740A=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.573T=0.426
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.805T=0.195
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
rs60390050.00073alcohol dependence20201924

eQTL of rs6039005 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 rs6039005 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 )
chr201325720413257264E07019495
chr201325772313258152E07020014
chr201323012313230420E081-7289
chr201323047613230838E081-6871
chr201325483213255634E08117123
chr201323089713231334E082-6375



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr201320034013202025E067-35684
chr201320210813202243E067-35466
chr201320224913203574E067-34135
chr201320034013202025E068-35684
chr201320224913203574E068-34135
chr201320034013202025E069-35684
chr201320224913203574E069-34135
chr201320210813202243E070-35466
chr201320224913203574E071-34135
chr201320034013202025E072-35684
chr201320210813202243E072-35466
chr201320224913203574E072-34135
chr201320034013202025E073-35684
chr201320224913203574E073-34135
chr201320210813202243E074-35466
chr201320210813202243E082-35466
chr201320224913203574E082-34135