rs11539983

Homo sapiens
T>C
SLC40A1 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0081 (2452/29952,GnomAD)
C=0122 (3566/29118,TOPMED)
C=0086 (432/5008,1000G)
C=0018 (71/3854,ALSPAC)
C=0022 (81/3708,TWINSUK)
chr2:189560748 (GRCh38.p7) (2q32.2)
AD
GWASdb2
1   publication(s)
See rs on genome
41 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.189560748T>C
GRCh37.p13 chr 2NC_000002.11:g.190425474T>C
SLC40A1 RefSeqGene LRG_837

Gene: SLC40A1, solute carrier family 40 member 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SLC40A1 transcriptNM_014585.5:c.N/A3 Prime UTR Variant
SLC40A1 transcript variant X1XM_005246505.1:c.N/A3 Prime UTR Variant
SLC40A1 transcript variant X2XM_017003938.1:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.729C=0.271
1000GenomesAmericanSub694T=0.970C=0.030
1000GenomesEast AsianSub1008T=0.999C=0.001
1000GenomesEuropeSub1006T=0.971C=0.029
1000GenomesGlobalStudy-wide5008T=0.914C=0.086
1000GenomesSouth AsianSub978T=0.980C=0.020
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.982C=0.018
The Genome Aggregation DatabaseAfricanSub8702T=0.760C=0.240
The Genome Aggregation DatabaseAmericanSub838T=0.970C=0.030
The Genome Aggregation DatabaseEast AsianSub1622T=1.000C=0.000
The Genome Aggregation DatabaseEuropeSub18488T=0.983C=0.017
The Genome Aggregation DatabaseGlobalStudy-wide29952T=0.918C=0.081
The Genome Aggregation DatabaseOtherSub302T=0.920C=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.877C=0.122
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.978C=0.022
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
rs115399830.00057alcohol dependence20201924

eQTL of rs11539983 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 rs11539983 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 )
chr2190424216190424865E068-609
chr2190434197190434257E0688723
chr2190434302190434500E0688828
chr2190442785190442846E06817311
chr2190424216190424865E069-609
chr2190424878190424976E069-498
chr2190424989190425072E069-402
chr2190434197190434257E0698723
chr2190434302190434500E0698828
chr2190441863190441940E06916389
chr2190442956190443019E06917482
chr2190443123190443230E06917649
chr2190379789190379848E071-45626
chr2190380095190380281E071-45193
chr2190380411190380459E071-45015
chr2190416817190416872E071-8602
chr2190416904190417018E071-8456
chr2190417074190417393E071-8081
chr2190417679190418194E071-7280
chr2190424216190424865E071-609
chr2190424878190424976E071-498
chr2190424989190425072E071-402
chr2190441222190441411E07115748
chr2190441863190441940E07116389
chr2190441978190442173E07116504
chr2190441863190441940E07216389
chr2190441978190442173E07216504
chr2190441978190442173E07316504
chr2190446913190447007E07321439
chr2190391921190392091E074-33383
chr2190413518190413644E074-11830
chr2190413863190414559E074-10915
chr2190424216190424865E074-609
chr2190446913190447007E07421439
chr2190420498190420622E081-4852
chr2190420768190421016E081-4458
chr2190420498190420622E082-4852
chr2190420768190421016E082-4458
chr2190441863190441940E08216389
chr2190441978190442173E08216504
chr2190442785190442846E08217311








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2190444250190444824E06718776
chr2190444872190446825E06719398
chr2190443418190443525E06817944
chr2190444250190444824E06818776
chr2190444872190446825E06819398
chr2190444872190446825E06919398
chr2190444250190444824E07018776
chr2190444872190446825E07019398
chr2190444250190444824E07118776
chr2190444872190446825E07119398
chr2190444250190444824E07218776
chr2190444872190446825E07219398
chr2190443418190443525E07317944
chr2190444250190444824E07318776
chr2190444872190446825E07319398
chr2190444250190444824E07418776
chr2190444872190446825E07419398
chr2190444250190444824E08218776
chr2190444872190446825E08219398