SNP Detail Info-rs2022443

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

VPS13A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0210 (6283/29924,GnomAD)
G=0203 (5927/29118,TOPMED)
G=0269 (1345/5008,1000G)
G=0231 (890/3854,ALSPAC)
G=0234 (867/3708,TWINSUK)

Position: chr9:77254936 (GRCh38.p7) (9q21.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Molecule type	Change	Amino acid[Codon]	SO Term
VPS13A transcript variant C	NM_001018037.1:c.	N/A	Intron Variant
VPS13A transcript variant D	NM_001018038.2:c.	N/A	Intron Variant
VPS13A transcript variant B	NM_015186.3:c.	N/A	Intron Variant
VPS13A transcript variant A	NM_033305.2:c.	N/A	Intron Variant
VPS13A transcript variant X1	XR_001746259.1:n.	N/A	Intron Variant
VPS13A transcript variant X2	XR_001746260.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.911	G=0.089
1000Genomes	American	Sub	694	T=0.620	G=0.380
1000Genomes	East Asian	Sub	1008	T=0.594	G=0.406
1000Genomes	Europe	Sub	1006	T=0.770	G=0.230
1000Genomes	Global	Study-wide	5008	T=0.731	G=0.269
1000Genomes	South Asian	Sub	978	T=0.670	G=0.330
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.769	G=0.231
The Genome Aggregation Database	African	Sub	8722	T=0.885	G=0.115
The Genome Aggregation Database	American	Sub	836	T=0.570	G=0.430
The Genome Aggregation Database	East Asian	Sub	1604	T=0.600	G=0.400
The Genome Aggregation Database	Europe	Sub	18460	T=0.771	G=0.228
The Genome Aggregation Database	Global	Study-wide	29924	T=0.790	G=0.210
The Genome Aggregation Database	Other	Sub	302	T=0.790	G=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.796	G=0.203
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.766	G=0.234

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet

SNP ID	p-value	Traits	Study
rs2022443	2.49E-05	nicotine dependence	17158188

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

rs2022443