rs9288497

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

VWC2L : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0238 (7137/29936,GnomAD)
G=0234 (6828/29118,TOPMED)
G=0243 (1219/5008,1000G)
G=0241 (929/3854,ALSPAC)
G=0233 (864/3708,TWINSUK)

Position: chr2:214505328 (GRCh38.p7) (2q35)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 56 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.214505328A>G
GRCh37.p13 chr 2	NC_000002.11:g.215370052A>G

Gene: VWC2L, von Willebrand factor C domain containing protein 2-like(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
VWC2L transcript	NM_001080500.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.776	G=0.224
1000Genomes	American	Sub	694	A=0.670	G=0.330
1000Genomes	East Asian	Sub	1008	A=0.737	G=0.263
1000Genomes	Europe	Sub	1006	A=0.769	G=0.231
1000Genomes	Global	Study-wide	5008	A=0.757	G=0.243
1000Genomes	South Asian	Sub	978	A=0.800	G=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.759	G=0.241
The Genome Aggregation Database	African	Sub	8708	A=0.784	G=0.216
The Genome Aggregation Database	American	Sub	834	A=0.690	G=0.310
The Genome Aggregation Database	East Asian	Sub	1618	A=0.717	G=0.283
The Genome Aggregation Database	Europe	Sub	18474	A=0.758	G=0.241
The Genome Aggregation Database	Global	Study-wide	29936	A=0.761	G=0.238
The Genome Aggregation Database	Other	Sub	302	A=0.720	G=0.280
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.765	G=0.234
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.767	G=0.233

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
rs9288497	0.00032	alcohol dependence(early age of onset)	20201924
rs9288497	0.00058	alcohol dependence	20201924

eQTL of rs9288497 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 rs9288497 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.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	215345728	215345883	E067	-24169
chr2	215346010	215346232	E067	-23820
chr2	215346603	215346744	E067	-23308
chr2	215347475	215347884	E067	-22168
chr2	215349103	215349270	E067	-20782
chr2	215379495	215379597	E067	9443
chr2	215379599	215379667	E067	9547
chr2	215330046	215330806	E068	-39246
chr2	215345728	215345883	E068	-24169
chr2	215346010	215346232	E068	-23820
chr2	215346603	215346744	E068	-23308
chr2	215347475	215347884	E068	-22168
chr2	215345728	215345883	E069	-24169
chr2	215346010	215346232	E069	-23820
chr2	215346603	215346744	E069	-23308
chr2	215379495	215379597	E069	9443
chr2	215379599	215379667	E069	9547
chr2	215407012	215407333	E069	36960
chr2	215410721	215411190	E069	40669
chr2	215411379	215411580	E069	41327
chr2	215379495	215379597	E070	9443
chr2	215379599	215379667	E070	9547
chr2	215380137	215380241	E070	10085
chr2	215407012	215407333	E070	36960
chr2	215414598	215415175	E070	44546
chr2	215345728	215345883	E071	-24169
chr2	215346010	215346232	E071	-23820
chr2	215346603	215346744	E071	-23308
chr2	215347475	215347884	E071	-22168
chr2	215349103	215349270	E071	-20782
chr2	215379599	215379667	E071	9547
chr2	215407012	215407333	E071	36960
chr2	215410721	215411190	E071	40669
chr2	215345728	215345883	E072	-24169
chr2	215346010	215346232	E072	-23820
chr2	215346603	215346744	E072	-23308
chr2	215347475	215347884	E072	-22168
chr2	215349103	215349270	E072	-20782
chr2	215379495	215379597	E072	9443
chr2	215379599	215379667	E072	9547
chr2	215380137	215380241	E072	10085
chr2	215407012	215407333	E072	36960
chr2	215346010	215346232	E073	-23820
chr2	215407012	215407333	E073	36960
chr2	215345728	215345883	E074	-24169
chr2	215346010	215346232	E074	-23820
chr2	215346603	215346744	E074	-23308
chr2	215379495	215379597	E081	9443
chr2	215379599	215379667	E081	9547
chr2	215410721	215411190	E081	40669
chr2	215411379	215411580	E081	41327
chr2	215412638	215412917	E081	42586
chr2	215414598	215415175	E081	44546
chr2	215407012	215407333	E082	36960
chr2	215410007	215410249	E082	39955
chr2	215410721	215411190	E082	40669