rs10460389

Homo sapiens
C>A
SLC39A10 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0037 (1137/29962,GnomAD)
A=0048 (1404/29118,TOPMED)
A=0051 (253/5008,1000G)
A=0002 (7/3854,ALSPAC)
A=0000 (0/3708,TWINSUK)
chr2:195641240 (GRCh38.p7) (2q32.3)
AD
GWASdb2
1   publication(s)
See rs on genome
29 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.195641240C>A
GRCh37.p13 chr 2NC_000002.11:g.196505964C>A

Gene: SLC39A10, solute carrier family 39 member 10(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SLC39A10 transcript variant 1NM_001127257.1:c.N/AGenic Upstream Transcript Variant
SLC39A10 transcript variant 2NM_020342.2:c.N/AGenic Upstream Transcript Variant
SLC39A10 transcript variant X2XM_011511504.2:c.N/AIntron Variant
SLC39A10 transcript variant X4XM_011511505.2:c.N/AIntron Variant
SLC39A10 transcript variant X1XM_005246689.4:c.N/AGenic Upstream Transcript Variant
SLC39A10 transcript variant X3XM_011511506.2:c.N/AGenic Upstream Transcript Variant
SLC39A10 transcript variant X5XM_011511507.2:c.N/AGenic Upstream Transcript Variant
SLC39A10 transcript variant X6XM_017004522.1:c.N/AGenic Upstream Transcript Variant
SLC39A10 transcript variant X7XM_017004523.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.888A=0.112
1000GenomesAmericanSub694C=0.970A=0.030
1000GenomesEast AsianSub1008C=0.932A=0.068
1000GenomesEuropeSub1006C=0.991A=0.009
1000GenomesGlobalStudy-wide5008C=0.949A=0.051
1000GenomesSouth AsianSub978C=0.990A=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.998A=0.002
The Genome Aggregation DatabaseAfricanSub8706C=0.903A=0.097
The Genome Aggregation DatabaseAmericanSub838C=0.950A=0.050
The Genome Aggregation DatabaseEast AsianSub1616C=0.933A=0.067
The Genome Aggregation DatabaseEuropeSub18500C=0.992A=0.007
The Genome Aggregation DatabaseGlobalStudy-wide29962C=0.962A=0.037
The Genome Aggregation DatabaseOtherSub302C=1.000A=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.951A=0.048
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=1.000A=0.000
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs104603890.000437alcohol dependence21314694

eQTL of rs10460389 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 rs10460389 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 )
chr2196530924196531064E06724960
chr2196531147196531249E06725183
chr2196552291196552796E06746327
chr2196531147196531249E06825183
chr2196551759196551919E06845795
chr2196552291196552796E06846327
chr2196532763196532990E06926799
chr2196530924196531064E07024960
chr2196531147196531249E07025183
chr2196551398196551453E07045434
chr2196551579196551657E07045615
chr2196551759196551919E07045795
chr2196552291196552796E07046327
chr2196532763196532990E07126799
chr2196552291196552796E07146327
chr2196530924196531064E07324960
chr2196531147196531249E07325183
chr2196530924196531064E07424960
chr2196531147196531249E07425183
chr2196456960196457073E081-48891
chr2196457113196457340E081-48624
chr2196477241196478162E081-27802
chr2196526812196526862E08120848
chr2196527010196527154E08121046
chr2196527701196527853E08121737
chr2196527862196528001E08121898
chr2196528041196528150E08122077
chr2196531147196531249E08125183
chr2196552291196552796E08246327









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2196520779196524508E06714815
chr2196520779196524508E06814815
chr2196520779196524508E06914815
chr2196520779196524508E07014815
chr2196520779196524508E07114815
chr2196520779196524508E07214815
chr2196520779196524508E07314815
chr2196520779196524508E07414815
chr2196520779196524508E08114815
chr2196520779196524508E08214815