rs2356261

Organism: Homo sapiens

Alleles: C>A / C>G / C>T

Gene : Feature

VPRBP : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0069 (2078/29916,GnomAD)
A=0148 (741/5008,1000G)
A=0019 (75/3854,ALSPAC)
A=0014 (53/3708,TWINSUK)

Position: chr3:51407713 (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.51407713C>A
GRCh38.p7 chr 3	NC_000003.12:g.51407713C>G
GRCh38.p7 chr 3	NC_000003.12:g.51407713C>T
GRCh37.p13 chr 3 fix patch HG186_PATCH	NW_003315910.1:g.29036C>A
GRCh37.p13 chr 3 fix patch HG186_PATCH	NW_003315910.1:g.29036C>G
GRCh37.p13 chr 3 fix patch HG186_PATCH	NW_003315910.1:g.29036C>T
GRCh37.p13 chr 3	NC_000003.11:g.51445146C>A
GRCh37.p13 chr 3	NC_000003.11:g.51445146C>G
GRCh37.p13 chr 3	NC_000003.11:g.51445146C>T

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	C=0.884	A=0.116
1000Genomes	American	Sub	694	C=0.760	A=0.240
1000Genomes	East Asian	Sub	1008	C=0.647	A=0.353
1000Genomes	Europe	Sub	1006	C=0.980	A=0.020
1000Genomes	Global	Study-wide	5008	C=0.852	A=0.148
1000Genomes	South Asian	Sub	978	C=0.960	A=0.040
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.981	A=0.019
The Genome Aggregation Database	African	Sub	8712	C=0.908	T=0.000
The Genome Aggregation Database	American	Sub	838	C=0.640	T=0.00,
The Genome Aggregation Database	East Asian	Sub	1610	C=0.659	T=0.000
The Genome Aggregation Database	Europe	Sub	18454	C=0.976	T=0.000
The Genome Aggregation Database	Global	Study-wide	29916	C=0.930	T=0.000
The Genome Aggregation Database	Other	Sub	302	C=0.980	T=0.00,
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.986	A=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
rs2356261	0.000127	alcohol dependence	20201924

eQTL of rs2356261 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 rs2356261 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.