SNP Detail Info-rs3176874

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

VCAM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0119 (3580/29960,GnomAD)
G=0102 (2997/29118,TOPMED)
G=0150 (749/5008,1000G)
G=0125 (481/3854,ALSPAC)
G=0126 (467/3708,TWINSUK)

Position: chr1:100734330 (GRCh38.p7) (1p21.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 2 Enhancers around

Promoter: 27 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
VCAM1 transcript variant 1	NM_001078.3:c.	N/A	Intron Variant
VCAM1 transcript variant 3	NM_001199834.1:c.	N/A	Intron Variant
VCAM1 transcript variant 2	NM_080682.2:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.949	G=0.051
1000Genomes	American	Sub	694	A=0.840	G=0.160
1000Genomes	East Asian	Sub	1008	A=0.774	G=0.226
1000Genomes	Europe	Sub	1006	A=0.861	G=0.139
1000Genomes	Global	Study-wide	5008	A=0.850	G=0.150
1000Genomes	South Asian	Sub	978	A=0.790	G=0.210
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.875	G=0.125
The Genome Aggregation Database	African	Sub	8732	A=0.931	G=0.069
The Genome Aggregation Database	American	Sub	838	A=0.790	G=0.210
The Genome Aggregation Database	East Asian	Sub	1600	A=0.802	G=0.198
The Genome Aggregation Database	Europe	Sub	18488	A=0.868	G=0.131
The Genome Aggregation Database	Global	Study-wide	29960	A=0.880	G=0.119
The Genome Aggregation Database	Other	Sub	302	A=0.840	G=0.160
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.897	G=0.102
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.874	G=0.126

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res

SNP ID	p-value	Traits	Study
rs3176874	2.18E-05	alcohol dependence	21703634

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	101200868	101201115	E068	982
chr1	101201337	101201389	E068	1451

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	101184793	101185615	E068	-14271
chr1	101185761	101185970	E068	-13916
chr1	101186902	101188096	E068	-11790
chr1	101186035	101186191	E069	-13695
chr1	101184793	101185615	E070	-14271
chr1	101185761	101185970	E070	-13916
chr1	101186035	101186191	E070	-13695
chr1	101186335	101186708	E070	-13178
chr1	101186902	101188096	E070	-11790
chr1	101184793	101185615	E071	-14271
chr1	101185761	101185970	E071	-13916
chr1	101186035	101186191	E071	-13695
chr1	101186335	101186708	E071	-13178
chr1	101186902	101188096	E071	-11790
chr1	101184793	101185615	E073	-14271
chr1	101185761	101185970	E073	-13916
chr1	101185761	101185970	E074	-13916
chr1	101186902	101188096	E074	-11790
chr1	101188590	101188659	E074	-11227
chr1	101188660	101188844	E074	-11042
chr1	101184793	101185615	E081	-14271
chr1	101185761	101185970	E081	-13916
chr1	101184793	101185615	E082	-14271
chr1	101185761	101185970	E082	-13916
chr1	101186035	101186191	E082	-13695
chr1	101186335	101186708	E082	-13178
chr1	101186902	101188096	E082	-11790

rs3176874