SNP Detail Info-rs12380218

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

VPS13A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0187 (5603/29908,GnomAD)
G=0173 (5037/29118,TOPMED)
G=0242 (1214/5008,1000G)
G=0224 (863/3854,ALSPAC)
G=0229 (848/3708,TWINSUK)

Position: chr9:77320744 (GRCh38.p7) (9q21.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 3 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	A=0.974	G=0.026
1000Genomes	American	Sub	694	A=0.630	G=0.370
1000Genomes	East Asian	Sub	1008	A=0.611	G=0.389
1000Genomes	Europe	Sub	1006	A=0.778	G=0.222
1000Genomes	Global	Study-wide	5008	A=0.758	G=0.242
1000Genomes	South Asian	Sub	978	A=0.690	G=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.776	G=0.224
The Genome Aggregation Database	African	Sub	8724	A=0.948	G=0.052
The Genome Aggregation Database	American	Sub	832	A=0.580	G=0.420
The Genome Aggregation Database	East Asian	Sub	1606	A=0.611	G=0.389
The Genome Aggregation Database	Europe	Sub	18444	A=0.777	G=0.222
The Genome Aggregation Database	Global	Study-wide	29908	A=0.812	G=0.187
The Genome Aggregation Database	Other	Sub	302	A=0.790	G=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.827	G=0.173
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.771	G=0.229

PMID	Title	Author	Journal
18565990	Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence.	Saccone SF	Bioinformatics
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet
18783506	Association of a single nucleotide polymorphism in neuronal acetylcholine receptor subunit alpha 5 (CHRNA5) with smoking status and with 'pleasurable buzz' during early experimentation with smoking.	Sherva R	Addiction

SNP ID	p-value	Traits	Study
rs12380218	2.09E-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

rs12380218