SNP Detail Info-rs13009774

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

VPS54 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0195 (5866/29958,GnomAD)
G=0138 (4027/29116,TOPMED)
G=0103 (516/5008,1000G)
G=0248 (955/3854,ALSPAC)
G=0253 (939/3708,TWINSUK)

Position: chr2:63977706 (GRCh38.p7) (2p14)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 25 Enhancers around

Promoter: 19 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
VPS54 transcript variant 2	NM_001005739.1:c.	N/A	Intron Variant
VPS54 transcript variant 1	NM_016516.2:c.	N/A	Intron Variant
VPS54 transcript variant X1	XM_006712029.3:c.	N/A	Intron Variant
VPS54 transcript variant X1	XM_017004316.1:c.	N/A	Intron Variant
VPS54 transcript variant X4	XR_001738770.1:n.	N/A	Intron Variant
VPS54 transcript variant X3	XR_244939.4:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.986	G=0.014
1000Genomes	American	Sub	694	T=0.800	G=0.200
1000Genomes	East Asian	Sub	1008	T=0.924	G=0.076
1000Genomes	Europe	Sub	1006	T=0.793	G=0.207
1000Genomes	Global	Study-wide	5008	T=0.897	G=0.103
1000Genomes	South Asian	Sub	978	T=0.930	G=0.070
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.752	G=0.248
The Genome Aggregation Database	African	Sub	8730	T=0.953	G=0.047
The Genome Aggregation Database	American	Sub	836	T=0.810	G=0.190
The Genome Aggregation Database	East Asian	Sub	1622	T=0.925	G=0.075
The Genome Aggregation Database	Europe	Sub	18468	T=0.721	G=0.278
The Genome Aggregation Database	Global	Study-wide	29958	T=0.804	G=0.195
The Genome Aggregation Database	Other	Sub	302	T=0.870	G=0.130
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.861	G=0.138
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.747	G=0.253

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
rs13009774	0.00092	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 )
chr2	64242628	64242803	E067	37788
chr2	64242956	64243073	E067	38116
chr2	64243190	64243254	E067	38350
chr2	64243332	64243382	E067	38492
chr2	64212898	64212972	E068	8058
chr2	64213791	64213841	E068	8951
chr2	64229036	64229086	E068	24196
chr2	64242628	64242803	E068	37788
chr2	64242956	64243073	E068	38116
chr2	64243190	64243254	E068	38350
chr2	64243332	64243382	E068	38492
chr2	64221390	64221515	E069	16550
chr2	64242628	64242803	E069	37788
chr2	64243190	64243254	E069	38350
chr2	64243332	64243382	E069	38492
chr2	64213791	64213841	E071	8951
chr2	64239130	64239570	E072	34290
chr2	64242628	64242803	E072	37788
chr2	64243190	64243254	E072	38350
chr2	64243332	64243382	E072	38492
chr2	64229036	64229086	E073	24196
chr2	64212898	64212972	E074	8058
chr2	64213791	64213841	E074	8951
chr2	64229036	64229086	E074	24196
chr2	64243332	64243382	E074	38492

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	64244765	64244828	E067	39925
chr2	64244973	64247946	E067	40133
chr2	64244765	64244828	E068	39925
chr2	64244973	64247946	E068	40133
chr2	64244765	64244828	E069	39925
chr2	64244973	64247946	E069	40133
chr2	64244765	64244828	E070	39925
chr2	64244973	64247946	E070	40133
chr2	64244765	64244828	E071	39925
chr2	64244973	64247946	E071	40133
chr2	64244765	64244828	E072	39925
chr2	64244973	64247946	E072	40133
chr2	64244765	64244828	E073	39925
chr2	64244973	64247946	E073	40133
chr2	64244973	64247946	E074	40133
chr2	64244765	64244828	E081	39925
chr2	64244973	64247946	E081	40133
chr2	64244765	64244828	E082	39925
chr2	64244973	64247946	E082	40133

rs13009774