rs12229376

Homo sapiens
G>T
SOX5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0038 (1123/29424,GnomAD)
T=0027 (790/29118,TOPMED)
T=0108 (540/5008,1000G)
T=0005 (20/3854,ALSPAC)
T=0008 (29/3708,TWINSUK)
chr12:23976502 (GRCh38.p7) (12p12.1)
AD
GWASdb2
1   publication(s)
See rs on genome
27 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.23976502G>T
GRCh37.p13 chr 12NC_000012.11:g.24129436G>T
SOX5 RefSeqGeneNG_029612.1:g.590945C>A

Gene: SOX5, SRY-box 5(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SOX5 transcript variant 4NM_001261414.1:c.N/AIntron Variant
SOX5 transcript variant 2NM_152989.3:c.N/AIntron Variant
SOX5 transcript variant 5NM_001261415.1:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant 1NM_006940.4:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant 3NM_178010.2:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X13XM_011520834.2:c.N/AIntron Variant
SOX5 transcript variant X12XM_011520835.2:c.N/AIntron Variant
SOX5 transcript variant X5XM_017019890.1:c.N/AIntron Variant
SOX5 transcript variant X6XM_017019891.1:c.N/AIntron Variant
SOX5 transcript variant X8XM_017019892.1:c.N/AIntron Variant
SOX5 transcript variant X19XM_017019893.1:c.N/AIntron Variant
SOX5 transcript variant X20XM_017019894.1:c.N/AIntron Variant
SOX5 transcript variant X23XM_017019896.1:c.N/AIntron Variant
SOX5 transcript variant X27XM_017019897.1:c.N/AIntron Variant
SOX5 transcript variant X31XM_017019898.1:c.N/AIntron Variant
SOX5 transcript variant X32XM_017019899.1:c.N/AIntron Variant
SOX5 transcript variant X16XM_011520831.2:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X3XM_011520832.2:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X4XM_011520833.2:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X22XM_011520837.2:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X26XM_011520838.2:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X37XM_011520842.2:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X1XM_017019888.1:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X2XM_017019889.1:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X21XM_017019895.1:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X33XM_017019900.1:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X34XM_017019901.1:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X35XM_017019902.1:c.N/AGenic Upstream Transcript Variant
SOX5 transcript variant X36XM_017019903.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.998T=0.002
1000GenomesAmericanSub694G=0.900T=0.100
1000GenomesEast AsianSub1008G=0.624T=0.376
1000GenomesEuropeSub1006G=0.994T=0.006
1000GenomesGlobalStudy-wide5008G=0.892T=0.108
1000GenomesSouth AsianSub978G=0.920T=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.995T=0.005
The Genome Aggregation DatabaseAfricanSub8656G=0.994T=0.006
The Genome Aggregation DatabaseAmericanSub816G=0.870T=0.130
The Genome Aggregation DatabaseEast AsianSub1592G=0.611T=0.389
The Genome Aggregation DatabaseEuropeSub18058G=0.981T=0.018
The Genome Aggregation DatabaseGlobalStudy-wide29424G=0.961T=0.038
The Genome Aggregation DatabaseOtherSub302G=0.970T=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.972T=0.027
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.992T=0.008
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs122293760.000935alcohol dependence24277619

eQTL of rs12229376 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 rs12229376 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 )
chr122416866024168923E06739224
chr122416728524167817E06837849
chr122417323424173529E06843798
chr122417356524173721E06844129
chr122416783624168598E06938400
chr122416866024168923E06939224
chr122408229024082361E070-47075
chr122408842724088479E070-40957
chr122416718724167271E07037751
chr122416728524167817E07037849
chr122417017424170233E07040738
chr122416728524167817E07137849
chr122416783624168598E07138400
chr122416866024168923E07139224
chr122417323424173529E07143798
chr122417356524173721E07144129
chr122416783624168598E07238400
chr122416866024168923E07239224
chr122416728524167817E07437849
chr122416783624168598E07438400
chr122416866024168923E07439224
chr122408822124088271E081-41165
chr122408842724088479E081-40957
chr122408891624088964E081-40472
chr122408842724088479E082-40957
chr122416783624168598E08238400
chr122416866024168923E08239224









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr122410114824101933E067-27503
chr122410198424104427E067-25009
chr122410114824101933E068-27503
chr122410198424104427E068-25009
chr122409652724096850E069-32586
chr122410114824101933E069-27503
chr122410198424104427E069-25009
chr122409652724096850E070-32586
chr122410085324101024E070-28412
chr122410114824101933E070-27503
chr122410198424104427E070-25009
chr122410114824101933E071-27503
chr122410198424104427E071-25009
chr122410114824101933E072-27503
chr122410198424104427E072-25009
chr122409652724096850E073-32586
chr122410114824101933E073-27503
chr122410198424104427E073-25009
chr122410114824101933E074-27503
chr122410198424104427E074-25009
chr122409652724096850E081-32586
chr122410085324101024E081-28412
chr122410114824101933E081-27503
chr122410198424104427E081-25009
chr122408990724090027E082-39409
chr122409652724096850E082-32586
chr122410085324101024E082-28412
chr122410114824101933E082-27503
chr122410198424104427E082-25009