SNP Detail Info-rs1278530

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

DMRTA2 : 2KB Upstream Variant
LOC105378714 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0470 (14063/29890,GnomAD)
G==0458 (13341/29118,TOPMED)
A=0420 (2104/5008,1000G)
A=0461 (1777/3854,ALSPAC)
A=0474 (1756/3708,TWINSUK)

Position: chr1:50423583 (GRCh38.p7) (1p32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 2 Enhancers around

Promoter: 9 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.50423583G>A
GRCh37.p13 chr 1	NC_000001.10:g.50889255G>A

Molecule type	Change	Amino acid[Codon]	SO Term
DMRTA2 transcript	NM_032110.2:c.	N/A	Upstream Transcript Variant
DMRTA2 transcript variant X1	XM_011541937.2:c.	N/A	Upstream Transcript Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378714 transcript	XR_947325.2:n.82G>A	G>A	Non Coding Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.346	A=0.654
1000Genomes	American	Sub	694	G=0.650	A=0.350
1000Genomes	East Asian	Sub	1008	G=0.843	A=0.157
1000Genomes	Europe	Sub	1006	G=0.537	A=0.463
1000Genomes	Global	Study-wide	5008	G=0.580	A=0.420
1000Genomes	South Asian	Sub	978	G=0.620	A=0.380
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.539	A=0.461
The Genome Aggregation Database	African	Sub	8692	G=0.357	A=0.643
The Genome Aggregation Database	American	Sub	838	G=0.710	A=0.290
The Genome Aggregation Database	East Asian	Sub	1620	G=0.810	A=0.190
The Genome Aggregation Database	Europe	Sub	18438	G=0.579	A=0.420
The Genome Aggregation Database	Global	Study-wide	29890	G=0.529	A=0.470
The Genome Aggregation Database	Other	Sub	302	G=0.450	A=0.550
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.458	A=0.541
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.526	A=0.474

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs1278530	0.00014	alcohol dependence(early age of onset)	20201924
rs1278530	0.00016	alcohol dependence	20201924

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

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	50927374	50927559	E071	38119
chr1	50927374	50927559	E074	38119

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	50888008	50889589	E067	0
chr1	50888008	50889589	E069	0
chr1	50884247	50884754	E070	-4501
chr1	50884247	50884754	E071	-4501
chr1	50888008	50889589	E072	0
chr1	50888008	50889589	E073	0
chr1	50888008	50889589	E074	0
chr1	50884247	50884754	E082	-4501
chr1	50888008	50889589	E082	0

rs1278530