rs12500169

Homo sapiens
C>G / C>T
SCD5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0069 (2092/29974,GnomAD)
G=0063 (1853/29118,TOPMED)
G=0096 (482/5008,1000G)
G=0066 (254/3854,ALSPAC)
G=0066 (244/3708,TWINSUK)
chr4:82723573 (GRCh38.p7) (4q21.22)
AD
GWASdb2
1   publication(s)
See rs on genome
8 Enhancers around
36 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.82723573C>G
GRCh38.p7 chr 4NC_000004.12:g.82723573C>T
GRCh37.p13 chr 4NC_000004.11:g.83644726C>G
GRCh37.p13 chr 4NC_000004.11:g.83644726C>T

Gene: SCD5, stearoyl-CoA desaturase 5(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SCD5 transcript variant 1NM_001037582.2:c.N/AIntron Variant
SCD5 transcript variant 2NM_024906.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.928G=0.072
1000GenomesAmericanSub694C=0.860G=0.140
1000GenomesEast AsianSub1008C=0.901G=0.099
1000GenomesEuropeSub1006C=0.930G=0.070
1000GenomesGlobalStudy-wide5008C=0.904G=0.096
1000GenomesSouth AsianSub978C=0.880G=0.120
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.934G=0.066
The Genome Aggregation DatabaseAfricanSub8728C=0.936G=0.064
The Genome Aggregation DatabaseAmericanSub838C=0.870G=0.13,
The Genome Aggregation DatabaseEast AsianSub1620C=0.920G=0.080
The Genome Aggregation DatabaseEuropeSub18486C=0.931G=0.068
The Genome Aggregation DatabaseGlobalStudy-wide29974C=0.930G=0.069
The Genome Aggregation DatabaseOtherSub302C=0.930G=0.07,
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.936G=0.063
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.934G=0.066
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
rs125001690.000698alcohol dependence21314694

eQTL of rs12500169 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 rs12500169 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 )
chr44133153641331702E06844479
chr44128304041283515E071-3542
chr44132803541328099E07140978
chr44132810141328161E07141044
chr44133153641331702E07144479
chr44128304041283515E074-3542
chr44133153641331702E07444479
chr44128304041283515E081-3542




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr44125794941258187E067-28870
chr44125821941260231E067-26826
chr44126027341260387E067-26670
chr44126051541260673E067-26384
chr44125794941258187E068-28870
chr44125821941260231E068-26826
chr44126027341260387E068-26670
chr44126051541260673E068-26384
chr44125794941258187E069-28870
chr44125821941260231E069-26826
chr44126027341260387E069-26670
chr44126051541260673E069-26384
chr44125794941258187E070-28870
chr44125821941260231E070-26826
chr44126027341260387E070-26670
chr44126051541260673E070-26384
chr44125821941260231E071-26826
chr44126027341260387E071-26670
chr44126051541260673E071-26384
chr44125794941258187E072-28870
chr44125821941260231E072-26826
chr44126027341260387E072-26670
chr44126051541260673E072-26384
chr44125794941258187E073-28870
chr44125821941260231E073-26826
chr44126027341260387E073-26670
chr44126051541260673E073-26384
chr44125821941260231E074-26826
chr44125794941258187E081-28870
chr44125821941260231E081-26826
chr44126027341260387E081-26670
chr44126051541260673E081-26384
chr44125794941258187E082-28870
chr44125821941260231E082-26826
chr44126027341260387E082-26670
chr44126051541260673E082-26384