rs56113850

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CYP2A6 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0491 (14590/29684,GnomAD)
C=0458 (2292/5008,1000G)
T==0417 (1608/3854,ALSPAC)
T==0426 (1581/3708,TWINSUK)

Position: chr19:40847202 (GRCh38.p7) (19q13.2)

Phenotype: ND

Dataset:

GWASCatalog

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 181 Enhancers around

Promoter: 32 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.40847202T>C
GRCh37.p13 chr 19	NC_000019.9:g.41353107T>C
CYP2A6 RefSeqGene	NG_008377.1:g.8246A>G

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.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.634	C=0.366
1000Genomes	American	Sub	694	T=0.350	C=0.650
1000Genomes	East Asian	Sub	1008	T=0.660	C=0.340
1000Genomes	Europe	Sub	1006	T=0.408	C=0.592
1000Genomes	Global	Study-wide	5008	T=0.542	C=0.458
1000Genomes	South Asian	Sub	978	T=0.580	C=0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.417	C=0.583
The Genome Aggregation Database	African	Sub	8608	T=0.607	C=0.393
The Genome Aggregation Database	American	Sub	834	T=0.380	C=0.620
The Genome Aggregation Database	East Asian	Sub	1564	T=0.701	C=0.299
The Genome Aggregation Database	Europe	Sub	18376	T=0.425	C=0.574
The Genome Aggregation Database	Global	Study-wide	29684	T=0.491	C=0.508
The Genome Aggregation Database	Other	Sub	302	T=0.410	C=0.590
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.426	C=0.574

PMID	Title	Author	Journal
27113016	Genome-Wide Association of the Laboratory-Based Nicotine Metabolite Ratio in Three Ancestries.	Baurley JW	Nicotine Tob Res
27488534	Novel Association of Genetic Markers Affecting CYP2A6 Activity and Lung Cancer Risk.	Patel YM	Cancer Res
27166759	Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions.	Yang J	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs56113850	1E-50	nicotine metabolite ratio in current smokers	27488534

eQTL of rs56113850 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 rs56113850 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.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr19	41309197	41310378	E067	-42729
chr19	41310386	41310560	E067	-42547
chr19	41310588	41311205	E067	-41902
chr19	41311222	41311679	E067	-41428
chr19	41311756	41311846	E067	-41261
chr19	41311901	41311984	E067	-41123
chr19	41314057	41314164	E067	-38943
chr19	41314165	41314366	E067	-38741
chr19	41314383	41314438	E067	-38669
chr19	41314543	41314844	E067	-38263
chr19	41318614	41318775	E067	-34332
chr19	41318893	41318990	E067	-34117
chr19	41319058	41319424	E067	-33683
chr19	41319757	41319828	E067	-33279
chr19	41324139	41324179	E067	-28928
chr19	41324351	41324854	E067	-28253
chr19	41324907	41325135	E067	-27972
chr19	41325420	41326011	E067	-27096
chr19	41328596	41329263	E067	-23844
chr19	41333021	41333471	E067	-19636
chr19	41310386	41310560	E068	-42547
chr19	41310588	41311205	E068	-41902
chr19	41311222	41311679	E068	-41428
chr19	41311756	41311846	E068	-41261
chr19	41311901	41311984	E068	-41123
chr19	41313359	41314035	E068	-39072
chr19	41315417	41315497	E068	-37610
chr19	41315541	41315630	E068	-37477
chr19	41315675	41315793	E068	-37314
chr19	41318461	41318553	E068	-34554
chr19	41318614	41318775	E068	-34332
chr19	41318893	41318990	E068	-34117
chr19	41324907	41325135	E068	-27972
chr19	41325420	41326011	E068	-27096
chr19	41328596	41329263	E068	-23844
chr19	41333021	41333471	E068	-19636
chr19	41307265	41307523	E069	-45584
chr19	41310588	41311205	E069	-41902
chr19	41311222	41311679	E069	-41428
chr19	41311756	41311846	E069	-41261
chr19	41311901	41311984	E069	-41123
chr19	41313359	41314035	E069	-39072
chr19	41315171	41315349	E069	-37758
chr19	41315417	41315497	E069	-37610
chr19	41315541	41315630	E069	-37477
chr19	41315675	41315793	E069	-37314
chr19	41319058	41319424	E069	-33683
chr19	41319502	41319594	E069	-33513
chr19	41319632	41319711	E069	-33396
chr19	41323661	41323817	E069	-29290
chr19	41323901	41323956	E069	-29151
chr19	41324139	41324179	E069	-28928
chr19	41324351	41324854	E069	-28253
chr19	41324907	41325135	E069	-27972
chr19	41325420	41326011	E069	-27096
chr19	41328368	41328433	E069	-24674
chr19	41328596	41329263	E069	-23844
chr19	41311222	41311679	E070	-41428
chr19	41311756	41311846	E070	-41261
chr19	41311901	41311984	E070	-41123
chr19	41313359	41314035	E070	-39072
chr19	41314057	41314164	E070	-38943
chr19	41339246	41339303	E070	-13804
chr19	41309197	41310378	E071	-42729
chr19	41310386	41310560	E071	-42547
chr19	41310588	41311205	E071	-41902
chr19	41311222	41311679	E071	-41428
chr19	41311756	41311846	E071	-41261
chr19	41311901	41311984	E071	-41123
chr19	41313359	41314035	E071	-39072
chr19	41314057	41314164	E071	-38943
chr19	41314165	41314366	E071	-38741
chr19	41314383	41314438	E071	-38669
chr19	41314543	41314844	E071	-38263
chr19	41314849	41314965	E071	-38142
chr19	41315171	41315349	E071	-37758
chr19	41315417	41315497	E071	-37610
chr19	41315541	41315630	E071	-37477
chr19	41315675	41315793	E071	-37314
chr19	41318461	41318553	E071	-34554
chr19	41318614	41318775	E071	-34332
chr19	41318893	41318990	E071	-34117
chr19	41319058	41319424	E071	-33683
chr19	41319502	41319594	E071	-33513
chr19	41319632	41319711	E071	-33396
chr19	41319757	41319828	E071	-33279
chr19	41319892	41320080	E071	-33027
chr19	41324139	41324179	E071	-28928
chr19	41324351	41324854	E071	-28253
chr19	41324907	41325135	E071	-27972
chr19	41325420	41326011	E071	-27096
chr19	41328368	41328433	E071	-24674
chr19	41328596	41329263	E071	-23844
chr19	41329354	41329411	E071	-23696
chr19	41309197	41310378	E072	-42729
chr19	41310386	41310560	E072	-42547
chr19	41310588	41311205	E072	-41902
chr19	41311222	41311679	E072	-41428
chr19	41311756	41311846	E072	-41261
chr19	41311901	41311984	E072	-41123
chr19	41313359	41314035	E072	-39072
chr19	41314057	41314164	E072	-38943
chr19	41314165	41314366	E072	-38741
chr19	41314383	41314438	E072	-38669
chr19	41314543	41314844	E072	-38263
chr19	41315541	41315630	E072	-37477
chr19	41315675	41315793	E072	-37314
chr19	41318461	41318553	E072	-34554
chr19	41324139	41324179	E072	-28928
chr19	41324907	41325135	E072	-27972
chr19	41328596	41329263	E072	-23844
chr19	41333021	41333471	E072	-19636
chr19	41339828	41339912	E072	-13195
chr19	41310588	41311205	E073	-41902
chr19	41311222	41311679	E073	-41428
chr19	41311756	41311846	E073	-41261
chr19	41311901	41311984	E073	-41123
chr19	41313359	41314035	E073	-39072
chr19	41318461	41318553	E073	-34554
chr19	41318614	41318775	E073	-34332
chr19	41318893	41318990	E073	-34117
chr19	41319058	41319424	E073	-33683
chr19	41324351	41324854	E073	-28253
chr19	41324907	41325135	E073	-27972
chr19	41328009	41328074	E073	-25033
chr19	41328217	41328302	E073	-24805
chr19	41328368	41328433	E073	-24674
chr19	41328596	41329263	E073	-23844
chr19	41333021	41333471	E073	-19636
chr19	41309197	41310378	E074	-42729
chr19	41310386	41310560	E074	-42547
chr19	41310588	41311205	E074	-41902
chr19	41311222	41311679	E074	-41428
chr19	41311756	41311846	E074	-41261
chr19	41311901	41311984	E074	-41123
chr19	41313359	41314035	E074	-39072
chr19	41314057	41314164	E074	-38943
chr19	41314165	41314366	E074	-38741
chr19	41314383	41314438	E074	-38669
chr19	41315541	41315630	E074	-37477
chr19	41315675	41315793	E074	-37314
chr19	41318461	41318553	E074	-34554
chr19	41318614	41318775	E074	-34332
chr19	41318893	41318990	E074	-34117
chr19	41319058	41319424	E074	-33683
chr19	41319502	41319594	E074	-33513
chr19	41319632	41319711	E074	-33396
chr19	41319757	41319828	E074	-33279
chr19	41319892	41320080	E074	-33027
chr19	41324139	41324179	E074	-28928
chr19	41324351	41324854	E074	-28253
chr19	41325420	41326011	E074	-27096
chr19	41328217	41328302	E074	-24805
chr19	41328368	41328433	E074	-24674
chr19	41328596	41329263	E074	-23844
chr19	41329354	41329411	E074	-23696
chr19	41333021	41333471	E074	-19636
chr19	41339246	41339303	E074	-13804
chr19	41339346	41339498	E074	-13609
chr19	41339828	41339912	E074	-13195
chr19	41354980	41355083	E074	1873
chr19	41306816	41307243	E081	-45864
chr19	41307265	41307523	E081	-45584
chr19	41309197	41310378	E081	-42729
chr19	41310386	41310560	E081	-42547
chr19	41310588	41311205	E081	-41902
chr19	41311222	41311679	E081	-41428
chr19	41311756	41311846	E081	-41261
chr19	41311901	41311984	E081	-41123
chr19	41312044	41313329	E081	-39778
chr19	41324351	41324854	E081	-28253
chr19	41311222	41311679	E082	-41428
chr19	41311756	41311846	E082	-41261
chr19	41311901	41311984	E082	-41123
chr19	41318461	41318553	E082	-34554
chr19	41318614	41318775	E082	-34332
chr19	41318893	41318990	E082	-34117
chr19	41323661	41323817	E082	-29290
chr19	41323901	41323956	E082	-29151
chr19	41324139	41324179	E082	-28928
chr19	41324351	41324854	E082	-28253

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	41303789	41306736	E067	-46371
chr19	41316570	41316987	E067	-36120
chr19	41317036	41317275	E067	-35832
chr19	41354337	41354458	E067	1230
chr19	41354484	41354854	E067	1377
chr19	41303789	41306736	E068	-46371
chr19	41316570	41316987	E068	-36120
chr19	41317036	41317275	E068	-35832
chr19	41303789	41306736	E069	-46371
chr19	41316570	41316987	E069	-36120
chr19	41317036	41317275	E069	-35832
chr19	41303789	41306736	E070	-46371
chr19	41316570	41316987	E070	-36120
chr19	41317036	41317275	E070	-35832
chr19	41354484	41354854	E070	1377
chr19	41303789	41306736	E071	-46371
chr19	41316570	41316987	E071	-36120
chr19	41317036	41317275	E071	-35832
chr19	41303789	41306736	E072	-46371
chr19	41316570	41316987	E072	-36120
chr19	41317036	41317275	E072	-35832
chr19	41354337	41354458	E072	1230
chr19	41354484	41354854	E072	1377
chr19	41303789	41306736	E073	-46371
chr19	41316570	41316987	E073	-36120
chr19	41317036	41317275	E073	-35832
chr19	41303789	41306736	E074	-46371
chr19	41316570	41316987	E074	-36120
chr19	41317036	41317275	E074	-35832
chr19	41303789	41306736	E082	-46371
chr19	41316570	41316987	E082	-36120
chr19	41317036	41317275	E082	-35832