rs12898460

Homo sapiens
C>T
C15orf53 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0219 (6563/29916,GnomAD)
T=0202 (5893/29118,TOPMED)
T=0159 (796/5008,1000G)
T=0311 (1200/3854,ALSPAC)
T=0316 (1172/3708,TWINSUK)
chr15:38694612 (GRCh38.p7) (15q14)
AD
GWASdb2
1   publication(s)
See rs on genome
8 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.38694612C>T
GRCh37.p13 chr 15NC_000015.9:g.38986813C>T

Gene: C15orf53, chromosome 15 open reading frame 53(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
C15orf53 transcriptNM_207444.2:c.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.949T=0.051
1000GenomesAmericanSub694C=0.750T=0.250
1000GenomesEast AsianSub1008C=0.900T=0.100
1000GenomesEuropeSub1006C=0.737T=0.263
1000GenomesGlobalStudy-wide5008C=0.841T=0.159
1000GenomesSouth AsianSub978C=0.810T=0.190
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.689T=0.311
The Genome Aggregation DatabaseAfricanSub8716C=0.903T=0.097
The Genome Aggregation DatabaseAmericanSub836C=0.750T=0.250
The Genome Aggregation DatabaseEast AsianSub1616C=0.908T=0.092
The Genome Aggregation DatabaseEuropeSub18446C=0.714T=0.286
The Genome Aggregation DatabaseGlobalStudy-wide29916C=0.780T=0.219
The Genome Aggregation DatabaseOtherSub302C=0.720T=0.280
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.797T=0.202
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.684T=0.316
PMID Title Author Journal
23089632A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.Wang JCMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs128984604.71E-08alcohol dependence23089632

eQTL of rs12898460 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 rs12898460 in Fetal Brain

Probe ID Position Gene beta p-value
cg21039679chr15:38989738C15orf53-0.02644457239366721.4963e-14

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 )
chr153896065238961725E068-25088
chr153896065238961725E069-25088
chr153896065238961725E070-25088
chr153894079638940926E071-45887
chr153900002839001434E08113215
chr153900646639007349E08119653
chr153896051838960573E082-26240
chr153896065238961725E082-25088