rs1503452

Homo sapiens
C>T
SOX6 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0315 (9443/29936,GnomAD)
T=0284 (8281/29118,TOPMED)
T=0231 (1158/5008,1000G)
T=0393 (1514/3854,ALSPAC)
T=0402 (1491/3708,TWINSUK)
chr11:16430585 (GRCh38.p7) (11p15.2)
AD
GWASdb2
2   publication(s)
See rs on genome
55 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.16430585C>T
GRCh37.p13 chr 11NC_000011.9:g.16452132C>T
SOX6 RefSeqGeneNG_012881.1:g.50804G>A

Gene: SOX6, SRY-box 6(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SOX6 transcript variant 2NM_033326.3:c.N/AIntron Variant
SOX6 transcript variant 3NM_001145811.1:c.N/AGenic Upstream Transcript Variant
SOX6 transcript variant 4NM_001145819.1:c.N/AGenic Upstream Transcript Variant
SOX6 transcript variant 1NM_017508.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.865T=0.135
1000GenomesAmericanSub694C=0.740T=0.260
1000GenomesEast AsianSub1008C=0.897T=0.103
1000GenomesEuropeSub1006C=0.593T=0.407
1000GenomesGlobalStudy-wide5008C=0.769T=0.231
1000GenomesSouth AsianSub978C=0.710T=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.607T=0.393
The Genome Aggregation DatabaseAfricanSub8716C=0.837T=0.163
The Genome Aggregation DatabaseAmericanSub834C=0.780T=0.220
The Genome Aggregation DatabaseEast AsianSub1614C=0.894T=0.106
The Genome Aggregation DatabaseEuropeSub18470C=0.592T=0.407
The Genome Aggregation DatabaseGlobalStudy-wide29936C=0.684T=0.315
The Genome Aggregation DatabaseOtherSub302C=0.540T=0.460
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.715T=0.284
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.598T=0.402
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
23691058Dosage transmission disequilibrium test (dTDT) for linkage and association detection.Zhang ZPLoS One

P-Value

SNP ID p-value Traits Study
rs15034520.00000321alcohol dependence23691058
rs15034520.00012alcohol dependence20201924

eQTL of rs1503452 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 rs1503452 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 )
chr111642420716424321E067-27811
chr111642434416425205E067-26927
chr111642521016425392E067-26740
chr111642553016425656E067-26476
chr111642521016425392E068-26740
chr111642698316427265E068-24867
chr111649160116491814E06839469
chr111649182416491930E06839692
chr111649196116492117E06839829
chr111649212316492552E06839991
chr111649265516492784E06840523
chr111649287216492954E06840740
chr111649317916493288E06841047
chr111641462116414720E070-37412
chr111641503716415153E070-36979
chr111642521016425392E070-26740
chr111642632716426377E070-25755
chr111642638116426605E070-25527
chr111642661516426698E070-25434
chr111642688616426963E070-25169
chr111642698316427265E070-24867
chr111643871216439091E070-13041
chr111647574316476284E07023611
chr111642393316424171E071-27961
chr111642420716424321E071-27811
chr111642521016425392E071-26740
chr111642553016425656E071-26476
chr111642590116425965E071-26167
chr111642612016426180E071-25952
chr111642632716426377E071-25755
chr111642638116426605E071-25527
chr111642661516426698E071-25434
chr111642688616426963E071-25169
chr111642698316427265E071-24867
chr111642521016425392E072-26740
chr111642553016425656E072-26476
chr111642688616426963E072-25169
chr111642335916423409E074-28723
chr111642353316423583E074-28549
chr111642375816423847E074-28285
chr111642393316424171E074-27961
chr111642420716424321E074-27811
chr111642434416425205E074-26927
chr111642612016426180E074-25952
chr111642632716426377E074-25755
chr111642638116426605E074-25527
chr111642661516426698E074-25434
chr111642688616426963E074-25169
chr111642698316427265E074-24867
chr111642638116426605E081-25527
chr111642661516426698E081-25434
chr111643871216439091E081-13041
chr111643871216439091E082-13041
chr111646217916462229E08210047
chr111646232916462437E08210197