SNP Detail Info-rs12916379

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

C15orf53 : 3 Prime UTR Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0214 (6418/29920,GnomAD)
G=0201 (5853/29118,TOPMED)
G=0146 (729/5008,1000G)
G=0309 (1190/3854,ALSPAC)
G=0307 (1138/3708,TWINSUK)

Position: chr15:38699319 (GRCh38.p7) (15q14)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 7 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.38699319A>G
GRCh37.p13 chr 15	NC_000015.9:g.38991520A>G

Molecule type	Change	Amino acid[Codon]	SO Term
C15orf53 transcript	NM_207444.2:c.	N/A	3 Prime UTR Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.948	G=0.052
1000Genomes	American	Sub	694	A=0.760	G=0.240
1000Genomes	East Asian	Sub	1008	A=0.965	G=0.035
1000Genomes	Europe	Sub	1006	A=0.739	G=0.261
1000Genomes	Global	Study-wide	5008	A=0.854	G=0.146
1000Genomes	South Asian	Sub	978	A=0.800	G=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.691	G=0.309
The Genome Aggregation Database	African	Sub	8714	A=0.903	G=0.097
The Genome Aggregation Database	American	Sub	836	A=0.760	G=0.240
The Genome Aggregation Database	East Asian	Sub	1622	A=0.972	G=0.028
The Genome Aggregation Database	Europe	Sub	18446	A=0.715	G=0.284
The Genome Aggregation Database	Global	Study-wide	29920	A=0.785	G=0.214
The Genome Aggregation Database	Other	Sub	302	A=0.730	G=0.270
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.799	G=0.201
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.693	G=0.307

PMID	Title	Author	Journal
23089632	A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.	Wang JC	Mol Psychiatry

SNP ID	p-value	Traits	Study
rs12916379	0.000000174	alcohol dependence	23089632
rs12916379	0.0000406	alcohol dependence	23089632

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
cg21039679	chr15:38989738	C15orf53	-0.026406344786987	1.0538e-14

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr15	38960652	38961725	E068	-29795
chr15	38960652	38961725	E069	-29795
chr15	38960652	38961725	E070	-29795
chr15	39000028	39001434	E081	8508
chr15	39006466	39007349	E081	14946
chr15	38960518	38960573	E082	-30947
chr15	38960652	38961725	E082	-29795

rs12916379