rs550338

Homo sapiens
G>A
SOX5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0300 (8989/29928,GnomAD)
A=0305 (8907/29118,TOPMED)
A=0467 (2340/5008,1000G)
A=0230 (888/3854,ALSPAC)
A=0224 (830/3708,TWINSUK)
chr12:24359103 (GRCh38.p7) (12p12.1)
AD
GWASdb2
1   publication(s)
See rs on genome
74 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.24359103G>A
GRCh37.p13 chr 12NC_000012.11:g.24512037G>A
SOX5 RefSeqGeneNG_029612.1:g.208344C>T

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 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 X20XM_017019894.1: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=0.697A=0.303
1000GenomesAmericanSub694G=0.460A=0.540
1000GenomesEast AsianSub1008G=0.235A=0.765
1000GenomesEuropeSub1006G=0.764A=0.236
1000GenomesGlobalStudy-wide5008G=0.533A=0.467
1000GenomesSouth AsianSub978G=0.430A=0.570
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.770A=0.230
The Genome Aggregation DatabaseAfricanSub8712G=0.707A=0.293
The Genome Aggregation DatabaseAmericanSub836G=0.420A=0.580
The Genome Aggregation DatabaseEast AsianSub1614G=0.198A=0.802
The Genome Aggregation DatabaseEuropeSub18464G=0.751A=0.248
The Genome Aggregation DatabaseGlobalStudy-wide29928G=0.699A=0.300
The Genome Aggregation DatabaseOtherSub302G=0.760A=0.240
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.694A=0.305
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.776A=0.224
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
rs5503380.0000888alcoholismpha002893
rs5503380.000089alcohol dependence20201924
rs5503380.00022alcohol dependence(early age of onset)20201924

eQTL of rs550338 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 rs550338 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 )
chr122453128124532359E06719244
chr122453238824532781E06720351
chr122454711424547468E06735077
chr122453128124532359E06819244
chr122453238824532781E06820351
chr122454608224546432E06834045
chr122454711424547468E06835077
chr122454810124548151E06836064
chr122454847124548609E06836434
chr122454861224548785E06836575
chr122454888724549032E06836850
chr122453128124532359E06919244
chr122453284724533544E06920810
chr122454608224546432E06934045
chr122454711424547468E06935077
chr122447134424471426E070-40611
chr122447144224471496E070-40541
chr122448095224481093E070-30944
chr122448117124481472E070-30565
chr122450954524509601E070-2436
chr122451542524515475E0703388
chr122451547824515589E0703441
chr122451608624516146E0704049
chr122451625824516361E0704221
chr122451645324516548E0704416
chr122452003124520359E0707994
chr122453075324531040E07018716
chr122453128124532359E07019244
chr122453238824532781E07020351
chr122453284724533544E07020810
chr122454847124548609E07036434
chr122454861224548785E07036575
chr122453128124532359E07119244
chr122453284724533544E07120810
chr122454847124548609E07136434
chr122454861224548785E07136575
chr122454711424547468E07235077
chr122454847124548609E07336434
chr122454861224548785E07336575
chr122454888724549032E07336850
chr122454608224546432E07434045
chr122454888724549032E07436850
chr122454908424549898E07437047
chr122447880424479090E081-32947
chr122447910424479154E081-32883
chr122447915924479203E081-32834
chr122447967224479722E081-32315
chr122453128124532359E08119244
chr122453238824532781E08120351
chr122453284724533544E08120810
chr122453362924533771E08121592
chr122453384924533938E08121812
chr122453395824534127E08121921
chr122453431324534536E08122276
chr122453465424534704E08122617
chr122454580924545863E08133772
chr122454589524546012E08133858
chr122454608224546432E08134045
chr122454711424547468E08135077
chr122454847124548609E08136434
chr122454861224548785E08136575
chr122454888724549032E08136850
chr122454908424549898E08137047
chr122453128124532359E08219244
chr122453238824532781E08220351
chr122453284724533544E08220810
chr122453362924533771E08221592
chr122453384924533938E08221812
chr122453395824534127E08221921
chr122453425824534308E08222221
chr122453431324534536E08222276
chr122454580924545863E08233772
chr122454589524546012E08233858
chr122454888724549032E08236850