rs1357251

Homo sapiens
T>C
SOX5 : Intron Variant
LOC101928471 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0134 (4033/29952,GnomAD)
C=0199 (5804/29118,TOPMED)
C=0146 (731/5008,1000G)
C=0043 (166/3854,ALSPAC)
C=0038 (141/3708,TWINSUK)
chr12:24222667 (GRCh38.p7) (12p12.1)
AD
GWASdb2
1   publication(s)
See rs on genome
129 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.24222667T>C
GRCh37.p13 chr 12NC_000012.11:g.24375601T>C
SOX5 RefSeqGeneNG_029612.1:g.344780A>G

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

Gene: LOC101928471, uncharacterized LOC101928471(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
SOX5-AS1 transcript variant 1NR_120472.1:n.N/AUpstream Transcript Variant
SOX5-AS1 transcript variant 2NR_120473.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.550C=0.450
1000GenomesAmericanSub694T=0.940C=0.060
1000GenomesEast AsianSub1008T=0.994C=0.006
1000GenomesEuropeSub1006T=0.954C=0.046
1000GenomesGlobalStudy-wide5008T=0.854C=0.146
1000GenomesSouth AsianSub978T=0.960C=0.040
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.957C=0.043
The Genome Aggregation DatabaseAfricanSub8698T=0.622C=0.378
The Genome Aggregation DatabaseAmericanSub838T=0.940C=0.060
The Genome Aggregation DatabaseEast AsianSub1622T=0.998C=0.002
The Genome Aggregation DatabaseEuropeSub18492T=0.963C=0.036
The Genome Aggregation DatabaseGlobalStudy-wide29952T=0.865C=0.134
The Genome Aggregation DatabaseOtherSub302T=0.950C=0.050
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.800C=0.199
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.962C=0.038
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
rs13572510.000765alcohol dependence20201924

eQTL of rs1357251 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 rs1357251 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 )
chr122437993924380253E0674338
chr122438036224380400E0674761
chr122438052624380784E0674925
chr122437544424375762E0680
chr122438081324381867E0685212
chr122438194724382076E0686346
chr122438212324382302E0686522
chr122438231424382706E0686713
chr122438288724382937E0687286
chr122438298624383382E0687385
chr122438340824383591E0687807
chr122438359524383678E0687994
chr122435218724352824E069-22777
chr122438194724382076E0696346
chr122438212324382302E0696522
chr122438231424382706E0696713
chr122438081324381867E0705212
chr122438194724382076E0706346
chr122438212324382302E0706522
chr122438231424382706E0706713
chr122438288724382937E0707286
chr122438298624383382E0707385
chr122440603524406103E07030434
chr122440835724408443E07032756
chr122440844724408667E07032846
chr122438081324381867E0715212
chr122438194724382076E0716346
chr122438212324382302E0716522
chr122438231424382706E0716713
chr122438194724382076E0726346
chr122438212324382302E0726522
chr122438231424382706E0726713
chr122437499524375072E073-529
chr122437544424375762E0730
chr122437993924380253E0734338
chr122438081324381867E0735212
chr122438194724382076E0736346
chr122438212324382302E0736522
chr122437484524374911E074-690
chr122437499524375072E074-529
chr122437544424375762E0740
chr122437579024376423E074189
chr122435044924350821E081-24780
chr122435082824350861E081-24740
chr122435104524351424E081-24177
chr122435142724351483E081-24118
chr122435171224351803E081-23798
chr122435184324351911E081-23690
chr122435196624352102E081-23499
chr122435218724352824E081-22777
chr122435286324353234E081-22367
chr122435336824353530E081-22071
chr122435372724353787E081-21814
chr122435390824353958E081-21643
chr122435755424357608E081-17993
chr122435762624357686E081-17915
chr122435789124358143E081-17458
chr122435819024358433E081-17168
chr122435883724359028E081-16573
chr122435903024359080E081-16521
chr122435921524359520E081-16081
chr122435958224359976E081-15625
chr122437683324376897E0811232
chr122437693924377183E0811338
chr122437742124377958E0811820
chr122437811224378205E0812511
chr122437993924380253E0814338
chr122438036224380400E0814761
chr122438052624380784E0814925
chr122438081324381867E0815212
chr122438194724382076E0816346
chr122438212324382302E0816522
chr122438231424382706E0816713
chr122438288724382937E0817286
chr122438298624383382E0817385
chr122438340824383591E0817807
chr122438359524383678E0817994
chr122439243124392481E08116830
chr122439775724398298E08122156
chr122439850724398568E08122906
chr122439915024399242E08123549
chr122439937224399841E08123771
chr122439991224400142E08124311
chr122440528324405496E08129682
chr122440550324405617E08129902
chr122440564224405997E08130041
chr122440603524406103E08130434
chr122435044924350821E082-24780
chr122435082824350861E082-24740
chr122435104524351424E082-24177
chr122435142724351483E082-24118
chr122435171224351803E082-23798
chr122435184324351911E082-23690
chr122435196624352102E082-23499
chr122435336824353530E082-22071
chr122435372724353787E082-21814
chr122435883724359028E082-16573
chr122435903024359080E082-16521
chr122435921524359520E082-16081
chr122435958224359976E082-15625
chr122437693924377183E0821338
chr122437742124377958E0821820
chr122437993924380253E0824338
chr122438036224380400E0824761
chr122438052624380784E0824925
chr122438081324381867E0825212
chr122438194724382076E0826346
chr122438212324382302E0826522
chr122438231424382706E0826713
chr122438288724382937E0827286
chr122438298624383382E0827385
chr122438340824383591E0827807
chr122438359524383678E0827994
chr122439361524393665E08218014
chr122439368524393747E08218084
chr122439731324397396E08221712
chr122439850724398568E08222906
chr122439915024399242E08223549
chr122439937224399841E08223771
chr122439991224400142E08224311
chr122440207624402207E08226475
chr122440259824402692E08226997
chr122440550324405617E08229902
chr122440564224405997E08230041
chr122440844724408667E08232846
chr122440901024409195E08233409
chr122440923924409561E08233638
chr122440965024409782E08234049
chr122440979724409992E08234196