rs56256500

Organism: Homo sapiens

Alleles: G>A / G>C / G>T

Gene : Feature

CYP2A6 : Missense Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0003 (108/29708,GnomAD)
A=0006 (199/29088,TOPMED)
G==0005 (70/13006,GO-ESP)
A=0005 (26/5008,1000G)

Position: chr19:40848266 (GRCh38.p7) (19q13.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.40848266G>A
GRCh38.p7 chr 19	NC_000019.10:g.40848266G>C
GRCh38.p7 chr 19	NC_000019.10:g.40848266G>T
GRCh37.p13 chr 19	NC_000019.9:g.41354171G>A
GRCh37.p13 chr 19	NC_000019.9:g.41354171G>C
GRCh37.p13 chr 19	NC_000019.9:g.41354171G>T
CYP2A6 RefSeqGene	NG_008377.1:g.7182C>T
CYP2A6 RefSeqGene	NG_008377.1:g.7182C>G
CYP2A6 RefSeqGene	NG_008377.1:g.7182C>A

Gene: CYP2A6, cytochrome P450 family 2 subfamily A member 6(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CYP2A6 transcript	NM_000762.5:c.607C>T	R [CGC]> C [TGC]	Coding Sequence Variant
cytochrome P450 2A6 precursor	NP_000753.3:p.Arg...NP_000753.3:p.Arg203Cys	R [Arg]> C [Cys]	Missense Variant
CYP2A6 transcript	NM_000762.5:c.607C>G	R [CGC]> G [GGC]	Coding Sequence Variant
cytochrome P450 2A6 precursor	NP_000753.3:p.Arg...NP_000753.3:p.Arg203Gly	R [Arg]> G [Gly]	Missense Variant
CYP2A6 transcript	NM_000762.5:c.607C>A	R [CGC]> S [AGC]	Coding Sequence Variant
cytochrome P450 2A6 precursor	NP_000753.3:p.Arg...NP_000753.3:p.Arg203Ser	R [Arg]> S [Ser]	Missense Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.980	A=0.020
1000Genomes	American	Sub	694	G=1.000	A=0.000
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=1.000	A=0.000
1000Genomes	Global	Study-wide	5008	G=0.995	A=0.005
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
The Genome Aggregation Database	African	Sub	8594	G=0.987	T=0.000
The Genome Aggregation Database	American	Sub	834	G=1.000	T=0.00,
The Genome Aggregation Database	East Asian	Sub	1576	G=1.000	T=0.000
The Genome Aggregation Database	Europe	Sub	18404	G=0.999	T=0.000
The Genome Aggregation Database	Global	Study-wide	29708	G=0.996	T=0.000
The Genome Aggregation Database	Other	Sub	300	G=1.000	T=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29088	G=0.993	A=0.006

PMID	Title	Author	Journal
18216723	A novel CYP2A6 allele, CYP2A6*23, impairs enzyme function in vitro and in vivo and decreases smoking in a population of Black-African descent.	Ho MK	Pharmacogenet Genomics
24944790	Screening for 392 polymorphisms in 141 pharmacogenes.	Kim JY	Biomed Rep
23130019	Frequencies of 23 functionally significant variant alleles related with metabolism of antineoplastic drugs in the chilean population: comparison with caucasian and asian populations.	Roco A	Front Genet

P-Value

SNP ID	p-value	Traits	Study
rs56256500	0.001	Drug response to nicotine	18216723

eQTL of rs56256500 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 rs56256500 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.