rs360534

Homo sapiens
G>A
SPTLC3 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0363 (10882/29934,GnomAD)
G==0365 (10651/29118,TOPMED)
G==0415 (2080/5008,1000G)
G==0379 (1459/3854,ALSPAC)
G==0385 (1428/3708,TWINSUK)
chr20:13007876 (GRCh38.p7) (20p12.1)
AD
GWASdb2
1   publication(s)
See rs on genome
29 Enhancers around
8 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.13007876G>A
GRCh37.p13 chr 20NC_000020.10:g.12988524G>A

Gene: SPTLC3, serine palmitoyltransferase long chain base subunit 3(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
SPTLC3 transcriptNM_018327.2:c.N/AUpstream Transcript Variant
SPTLC3 transcript variant X1XM_011529279.1:c.N/AUpstream Transcript Variant
SPTLC3 transcript variant X4XM_017027922.1:c.N/AUpstream Transcript Variant
SPTLC3 transcript variant X2XM_011529280.2:c.N/AN/A
SPTLC3 transcript variant X3XR_001754317.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.285A=0.715
1000GenomesAmericanSub694G=0.410A=0.590
1000GenomesEast AsianSub1008G=0.597A=0.403
1000GenomesEuropeSub1006G=0.347A=0.653
1000GenomesGlobalStudy-wide5008G=0.415A=0.585
1000GenomesSouth AsianSub978G=0.480A=0.520
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.379A=0.621
The Genome Aggregation DatabaseAfricanSub8716G=0.314A=0.686
The Genome Aggregation DatabaseAmericanSub836G=0.410A=0.590
The Genome Aggregation DatabaseEast AsianSub1612G=0.569A=0.431
The Genome Aggregation DatabaseEuropeSub18472G=0.367A=0.632
The Genome Aggregation DatabaseGlobalStudy-wide29934G=0.363A=0.636
The Genome Aggregation DatabaseOtherSub298G=0.300A=0.700
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.365A=0.634
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.385A=0.615
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs3605343.22E-05alcohol dependence21703634

eQTL of rs360534 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 rs360534 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 )
chr201299131412991443E0672790
chr201294563612945758E068-42766
chr201294576212945839E068-42685
chr201294622812946466E068-42058
chr201294656312946927E068-41597
chr201299131412991443E0682790
chr201294622812946466E069-42058
chr201294656312946927E069-41597
chr201299131412991443E0692790
chr201294622812946466E070-42058
chr201294563612945758E071-42766
chr201294576212945839E071-42685
chr201294622812946466E071-42058
chr201294576212945839E072-42685
chr201294622812946466E072-42058
chr201299131412991443E0722790
chr201299131412991443E0732790
chr201294622812946466E074-42058
chr201294656312946927E074-41597
chr201299131412991443E0742790
chr201294622812946466E081-42058
chr201294656312946927E081-41597
chr201294745412947562E081-40962
chr201294771212947787E081-40737
chr201294783012947882E081-40642
chr201294745412947562E082-40962
chr201294771212947787E082-40737
chr201297039712970884E082-17640
chr201297092712970981E082-17543










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr201298928912991109E067765
chr201298928912991109E068765
chr201298928912991109E069765
chr201298928912991109E071765
chr201298928912991109E072765
chr201298928912991109E073765
chr201298928912991109E074765
chr201298928912991109E081765