rs1543660

Homo sapiens
T>C
MTUS2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0058 (1751/29910,GnomAD)
C=0046 (1366/29116,TOPMED)
C=0146 (730/5008,1000G)
C=0024 (94/3854,ALSPAC)
C=0026 (95/3708,TWINSUK)
chr13:29281513 (GRCh38.p7) (13q12.3)
AD
GWASdb2
1   publication(s)
See rs on genome
31 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.29281513T>C
GRCh37.p13 chr 13NC_000013.10:g.29855650T>C

Gene: MTUS2, microtubule associated tumor suppressor candidate 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MTUS2 transcript variant 1NM_001033602.2:c.N/AIntron Variant
MTUS2 transcript variant 2NM_015233.5:c.N/AGenic Upstream Transcript Variant
MTUS2 transcript variant X1XM_011535019.2:c.N/AIntron Variant
MTUS2 transcript variant X2XM_011535020.2:c.N/AIntron Variant
MTUS2 transcript variant X3XM_011535021.2:c.N/AIntron Variant
MTUS2 transcript variant X7XM_011535022.2:c.N/AIntron Variant
MTUS2 transcript variant X4XM_017020500.1:c.N/AIntron Variant
MTUS2 transcript variant X5XM_017020501.1:c.N/AIntron Variant
MTUS2 transcript variant X6XM_017020502.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.930C=0.070
1000GenomesAmericanSub694T=0.970C=0.030
1000GenomesEast AsianSub1008T=0.695C=0.305
1000GenomesEuropeSub1006T=0.969C=0.031
1000GenomesGlobalStudy-wide5008T=0.854C=0.146
1000GenomesSouth AsianSub978T=0.710C=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.976C=0.024
The Genome Aggregation DatabaseAfricanSub8696T=0.933C=0.067
The Genome Aggregation DatabaseAmericanSub838T=0.980C=0.020
The Genome Aggregation DatabaseEast AsianSub1616T=0.723C=0.277
The Genome Aggregation DatabaseEuropeSub18458T=0.962C=0.037
The Genome Aggregation DatabaseGlobalStudy-wide29910T=0.941C=0.058
The Genome Aggregation DatabaseOtherSub302T=0.970C=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.953C=0.046
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.974C=0.026
PMID Title Author Journal
22072270Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms.Wang KSJ Neural Transm (Vienna)

P-Value

SNP ID p-value Traits Study
rs15436603.62E-05alcohol withdrawal symptoms22072270

eQTL of rs1543660 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 rs1543660 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 )
chr132985544729856741E0670
chr132988508429885250E06729434
chr132989275029893190E06737100
chr132989819429898309E06742544
chr132989257529892636E06836925
chr132989275029893190E06837100
chr132989257529892636E06936925
chr132989275029893190E06937100
chr132989819429898309E06942544
chr132989257529892636E07136925
chr132989355729893900E07137907
chr132988508429885250E07229434
chr132989257529892636E07236925
chr132989275029893190E07237100
chr132988508429885250E07429434
chr132989200629892233E07436356
chr132989257529892636E07436925
chr132989275029893190E07437100
chr132989355729893900E07437907
chr132989804529898115E07442395
chr132980642729806477E081-49173
chr132980654029806616E081-49034
chr132983467429834895E081-20755
chr132983494729835076E081-20574
chr132983513929835274E081-20376
chr132983538229835525E081-20125
chr132985544729856741E0810
chr132989257529892636E08136925
chr132989275029893190E08137100
chr132989355729893900E08137907
chr132985342529854277E082-1373