SNP Detail Info-rs34141940

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

C15orf53 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0243 (7288/29888,GnomAD)
A=0247 (7217/29118,TOPMED)
A=0177 (886/5008,1000G)
A=0311 (1197/3854,ALSPAC)
A=0314 (1164/3708,TWINSUK)

Position: chr15:38697456 (GRCh38.p7) (15q14)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 8 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.38697456G>A
GRCh37.p13 chr 15	NC_000015.9:g.38989657G>A

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

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.829	A=0.171
1000Genomes	American	Sub	694	G=0.750	A=0.250
1000Genomes	East Asian	Sub	1008	G=0.968	A=0.032
1000Genomes	Europe	Sub	1006	G=0.740	A=0.260
1000Genomes	Global	Study-wide	5008	G=0.823	A=0.177
1000Genomes	South Asian	Sub	978	G=0.800	A=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.689	A=0.311
The Genome Aggregation Database	African	Sub	8698	G=0.808	A=0.192
The Genome Aggregation Database	American	Sub	838	G=0.750	A=0.250
The Genome Aggregation Database	East Asian	Sub	1618	G=0.972	A=0.028
The Genome Aggregation Database	Europe	Sub	18434	G=0.713	A=0.286
The Genome Aggregation Database	Global	Study-wide	29888	G=0.756	A=0.243
The Genome Aggregation Database	Other	Sub	300	G=0.720	A=0.280
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.752	A=0.247
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.686	A=0.314

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
rs34141940	1.07E-07	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	-0.0271818148571393	4.9448e-16

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr15	38960652	38961725	E068	-27932
chr15	38960652	38961725	E069	-27932
chr15	38960652	38961725	E070	-27932
chr15	38940796	38940926	E071	-48731
chr15	39000028	39001434	E081	10371
chr15	39006466	39007349	E081	16809
chr15	38960518	38960573	E082	-29084
chr15	38960652	38961725	E082	-27932

rs34141940