rs11047279

Homo sapiens
C>T
SOX5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0233 (6986/29896,GnomAD)
T=0261 (7618/29118,TOPMED)
T=0232 (1161/5008,1000G)
T=0214 (823/3854,ALSPAC)
T=0200 (742/3708,TWINSUK)
chr12:24140368 (GRCh38.p7) (12p12.1)
ND
GWASdb2
1   publication(s)
See rs on genome
33 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.24140368C>T
GRCh37.p13 chr 12NC_000012.11:g.24293302C>T
SOX5 RefSeqGeneNG_029612.1:g.427079G>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 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
1000GenomesAfricanSub1322C=0.666T=0.334
1000GenomesAmericanSub694C=0.770T=0.230
1000GenomesEast AsianSub1008C=0.836T=0.164
1000GenomesEuropeSub1006C=0.774T=0.226
1000GenomesGlobalStudy-wide5008C=0.768T=0.232
1000GenomesSouth AsianSub978C=0.830T=0.170
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.786T=0.214
The Genome Aggregation DatabaseAfricanSub8704C=0.696T=0.304
The Genome Aggregation DatabaseAmericanSub836C=0.760T=0.240
The Genome Aggregation DatabaseEast AsianSub1614C=0.844T=0.156
The Genome Aggregation DatabaseEuropeSub18442C=0.792T=0.207
The Genome Aggregation DatabaseGlobalStudy-wide29896C=0.766T=0.233
The Genome Aggregation DatabaseOtherSub300C=0.800T=0.200
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.738T=0.261
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.800T=0.200
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs110472797E-05alcohol and nictotine co-dependence20158304

eQTL of rs11047279 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 rs11047279 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 )
chr122428676224287155E068-6147
chr122428727724287538E068-5764
chr122428962224289741E070-3561
chr122429076124290815E070-2487
chr122429090024291007E070-2295
chr122429106724291706E070-1596
chr122430592424306036E07012622
chr122430616024306330E07012858
chr122429090024291007E073-2295
chr122429106724291706E073-1596
chr122428908324289225E081-4077
chr122428933524289508E081-3794
chr122428962224289741E081-3561
chr122428988424290018E081-3284
chr122429010424290154E081-3148
chr122429076124290815E081-2487
chr122429090024291007E081-2295
chr122429106724291706E081-1596
chr122429323624293290E081-12
chr122424375224243945E082-49357
chr122428617724286718E082-6584
chr122428676224287155E082-6147
chr122428716324287259E082-6043
chr122428727724287538E082-5764
chr122428759524287708E082-5594
chr122428908324289225E082-4077
chr122428933524289508E082-3794
chr122428962224289741E082-3561
chr122428988424290018E082-3284
chr122429010424290154E082-3148
chr122429076124290815E082-2487
chr122429090024291007E082-2295
chr122429106724291706E082-1596