rs3792408

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

VPRBP : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0068 (2049/29976,GnomAD)
G=0081 (2359/29118,TOPMED)
G=0147 (734/5008,1000G)
G=0019 (75/3854,ALSPAC)
G=0014 (53/3708,TWINSUK)

Position: chr3:51400166 (GRCh38.p7) (3p21.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.51400166A>G
GRCh37.p13 chr 3 fix patch HG186_PATCH	NW_003315910.1:g.21489A>G
GRCh37.p13 chr 3	NC_000003.11:g.51437597A>G

Gene: VPRBP, Vpr (HIV-1) binding protein(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DCAF1 transcript variant 2	NM_001171904.1:c.	N/A	Intron Variant
DCAF1 transcript variant 1	NM_014703.2:c.	N/A	Intron Variant
VPRBP transcript variant X10	XM_005276753.4:c.	N/A	Intron Variant
VPRBP transcript variant X9	XM_005276755.4:c.	N/A	Intron Variant
VPRBP transcript variant X3	XM_011534273.2:c.	N/A	Intron Variant
VPRBP transcript variant X2	XM_011534274.2:c.	N/A	Intron Variant
VPRBP transcript variant X7	XM_011534275.2:c.	N/A	Intron Variant
VPRBP transcript variant X6	XM_011534276.2:c.	N/A	Intron Variant
VPRBP transcript variant X1	XM_011534277.2:c.	N/A	Intron Variant
VPRBP transcript variant X4	XM_017007546.1:c.	N/A	Intron Variant
VPRBP transcript variant X5	XM_017007547.1:c.	N/A	Intron Variant
VPRBP transcript variant X8	XM_017007548.1:c.	N/A	Intron Variant
VPRBP transcript variant X11	XM_017007549.1:c.	N/A	Intron Variant
VPRBP transcript variant X12	XM_017007550.1:c.	N/A	Intron Variant
VPRBP transcript variant X16	XM_017007551.1:c.	N/A	Intron Variant
VPRBP transcript variant X13	XR_001740385.1:n.	N/A	Intron Variant
VPRBP transcript variant X14	XR_001740386.1:n.	N/A	Intron Variant
VPRBP transcript variant X15	XR_001740387.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.890	G=0.110
1000Genomes	American	Sub	694	A=0.760	G=0.240
1000Genomes	East Asian	Sub	1008	A=0.647	G=0.353
1000Genomes	Europe	Sub	1006	A=0.980	G=0.020
1000Genomes	Global	Study-wide	5008	A=0.853	G=0.147
1000Genomes	South Asian	Sub	978	A=0.960	G=0.040
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.981	G=0.019
The Genome Aggregation Database	African	Sub	8720	A=0.911	G=0.089
The Genome Aggregation Database	American	Sub	838	A=0.640	G=0.360
The Genome Aggregation Database	East Asian	Sub	1614	A=0.660	G=0.340
The Genome Aggregation Database	Europe	Sub	18502	A=0.977	G=0.023
The Genome Aggregation Database	Global	Study-wide	29976	A=0.931	G=0.068
The Genome Aggregation Database	Other	Sub	302	A=0.980	G=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.919	G=0.081
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.986	G=0.014

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

P-Value

SNP ID	p-value	Traits	Study
rs3792408	0.000142	alcohol dependence	20201924

eQTL of rs3792408 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 rs3792408 in Fetal Brain

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

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.