SNP Detail Info-rs2002594

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

FAM162A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0406 (12131/29872,GnomAD)
A==0396 (11532/29118,TOPMED)
A==0392 (1963/5008,1000G)
A==0422 (1628/3854,ALSPAC)
A==0398 (1477/3708,TWINSUK)

Position: chr3:122392714 (GRCh38.p7) (3q21.1)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 29 Enhancers around

Promoter: 23 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.122392714A>G
GRCh37.p13 chr 3	NC_000003.11:g.122111561A>G

Molecule type	Change	Amino acid[Codon]	SO Term
FAM162A transcript	NM_014367.3:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.383	G=0.617
1000Genomes	American	Sub	694	A=0.540	G=0.460
1000Genomes	East Asian	Sub	1008	A=0.308	G=0.692
1000Genomes	Europe	Sub	1006	A=0.410	G=0.590
1000Genomes	Global	Study-wide	5008	A=0.392	G=0.608
1000Genomes	South Asian	Sub	978	A=0.370	G=0.630
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.422	G=0.578
The Genome Aggregation Database	African	Sub	8692	A=0.383	G=0.617
The Genome Aggregation Database	American	Sub	838	A=0.570	G=0.430
The Genome Aggregation Database	East Asian	Sub	1606	A=0.290	G=0.710
The Genome Aggregation Database	Europe	Sub	18434	A=0.418	G=0.581
The Genome Aggregation Database	Global	Study-wide	29872	A=0.406	G=0.593
The Genome Aggregation Database	Other	Sub	302	A=0.460	G=0.540
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.396	G=0.604
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.398	G=0.602

PMID	Title	Author	Journal
28990359	Ancestry-specific and sex-specific risk alleles identified in a genome-wide gene-by-alcohol dependence interaction study of risky sexual behaviors.	Polimanti R	Am J Med Genet B Neuropsychiatr Genet

SNP ID	p-value	Traits	Study
rs2002594	5E-08	alcohol dependence	28990359

eQTL of rs2002594 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr3:122111561	WDR5B	ENSG00000196981.2	A>G	9.4397e-8	-23321	Cerebellum
Chr3:122111561	KPNA1	ENSG00000114030.8	A>G	2.0096e-12	-122231	Cerebellum
Chr3:122111561	WDR5B	ENSG00000196981.2	A>G	2.5941e-4	-23321	Frontal_Cortex_BA9
Chr3:122111561	WDR5B	ENSG00000196981.2	A>G	5.5804e-6	-23321	Cortex
Chr3:122111561	KPNA1	ENSG00000114030.8	A>G	4.0597e-9	-122231	Cerebellar_Hemisphere
Chr3:122111561	WDR5B	ENSG00000196981.2	A>G	2.4741e-5	-23321	Anterior_cingulate_cortex
Chr3:122111561	WDR5B	ENSG00000196981.2	A>G	2.9732e-5	-23321	Nucleus_accumbens_basal_ganglia

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr3	122133383	122133522	E067	21822
chr3	122136294	122136348	E067	24733
chr3	122075405	122075550	E068	-36011
chr3	122133383	122133522	E068	21822
chr3	122133936	122133977	E068	22375
chr3	122136294	122136348	E068	24733
chr3	122111724	122111779	E069	163
chr3	122111816	122112074	E069	255
chr3	122112100	122112200	E069	539
chr3	122133383	122133522	E069	21822
chr3	122133936	122133977	E069	22375
chr3	122136294	122136348	E069	24733
chr3	122133383	122133522	E070	21822
chr3	122133936	122133977	E070	22375
chr3	122136294	122136348	E070	24733
chr3	122111816	122112074	E071	255
chr3	122112100	122112200	E071	539
chr3	122133383	122133522	E071	21822
chr3	122133936	122133977	E071	22375
chr3	122136294	122136348	E071	24733
chr3	122133383	122133522	E072	21822
chr3	122133936	122133977	E072	22375
chr3	122136294	122136348	E073	24733
chr3	122133936	122133977	E074	22375
chr3	122136294	122136348	E074	24733
chr3	122144001	122144041	E074	32440
chr3	122133383	122133522	E081	21822
chr3	122136294	122136348	E081	24733
chr3	122133936	122133977	E082	22375

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	122101352	122103792	E067	-7769
chr3	122104080	122104173	E067	-7388
chr3	122134137	122135804	E067	22576
chr3	122101352	122103792	E068	-7769
chr3	122134137	122135804	E068	22576
chr3	122101352	122103792	E069	-7769
chr3	122104080	122104173	E069	-7388
chr3	122134137	122135804	E069	22576
chr3	122101352	122103792	E070	-7769
chr3	122134137	122135804	E070	22576
chr3	122101352	122103792	E071	-7769
chr3	122134137	122135804	E071	22576
chr3	122101352	122103792	E072	-7769
chr3	122104080	122104173	E072	-7388
chr3	122134137	122135804	E072	22576
chr3	122101352	122103792	E073	-7769
chr3	122134137	122135804	E073	22576
chr3	122101352	122103792	E074	-7769
chr3	122134137	122135804	E074	22576
chr3	122101352	122103792	E081	-7769
chr3	122134137	122135804	E081	22576
chr3	122101352	122103792	E082	-7769
chr3	122134137	122135804	E082	22576

rs2002594