rs4079366

Organism: Homo sapiens

Alleles: T>A / T>C

Gene : Feature

CYP2A7 : Missense Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0196 (5842/29812,GnomAD)
C=0205 (2667/13004,GO-ESP)
T==0206 (1030/5008,1000G)
T==0257 (992/3854,ALSPAC)
T==0260 (963/3708,TWINSUK)

Position: chr19:40878770 (GRCh38.p7) (19q13.2)

Phenotype: ND

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 188 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.40878770T>A
GRCh38.p7 chr 19	NC_000019.10:g.40878770T>C
GRCh37.p13 chr 19	NC_000019.9:g.41384675T>A
GRCh37.p13 chr 19	NC_000019.9:g.41384675T>C
CYP2A7 RefSeqGene	NG_007960.1:g.8983A>T
CYP2A7 RefSeqGene	NG_007960.1:g.8983A>G

Gene: CYP2A7, cytochrome P450 family 2 subfamily A member 7(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CYP2A7 transcript variant 2	NM_030589.2:c.668A>T	H [CAC]> L [CTC]	Coding Sequence Variant
cytochrome P450 2A7 isoform 2 precursor	NP_085079.2:p.His...NP_085079.2:p.His223Leu	H [His]> L [Leu]	Missense Variant
CYP2A7 transcript variant 2	NM_030589.2:c.668A>G	H [CAC]> R [CGC]	Coding Sequence Variant
cytochrome P450 2A7 isoform 2 precursor	NP_085079.2:p.His...NP_085079.2:p.His223Arg	H [His]> R [Arg]	Missense Variant
CYP2A7 transcript variant 1	NM_000764.2:c.821A>T	H [CAC]> L [CTC]	Coding Sequence Variant
cytochrome P450 2A7 isoform 1 precursor	NP_000755.2:p.His...NP_000755.2:p.His274Leu	H [His]> L [Leu]	Missense Variant
CYP2A7 transcript variant 1	NM_000764.2:c.821A>G	H [CAC]> R [CGC]	Coding Sequence Variant
cytochrome P450 2A7 isoform 1 precursor	NP_000755.2:p.His...NP_000755.2:p.His274Arg	H [His]> R [Arg]	Missense Variant
CYP2A7 transcript variant X2	XM_017026383.1:c....XM_017026383.1:c.821A>T	H [CAC]> L [CTC]	Coding Sequence Variant
cytochrome P450 2A7 isoform X1	XP_016881872.1:p....XP_016881872.1:p.His274Leu	H [His]> L [Leu]	Missense Variant
CYP2A7 transcript variant X2	XM_017026383.1:c....XM_017026383.1:c.821A>G	H [CAC]> R [CGC]	Coding Sequence Variant
cytochrome P450 2A7 isoform X1	XP_016881872.1:p....XP_016881872.1:p.His274Arg	H [His]> R [Arg]	Missense Variant
CYP2A7 transcript variant X1	XR_935754.2:n.456...XR_935754.2:n.4563A>T	A>T	Non Coding Transcript Variant
CYP2A7 transcript variant X1	XR_935754.2:n.456...XR_935754.2:n.4563A>G	A>G	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.050	C=0.950
1000Genomes	American	Sub	694	T=0.180	C=0.820
1000Genomes	East Asian	Sub	1008	T=0.349	C=0.651
1000Genomes	Europe	Sub	1006	T=0.242	C=0.758
1000Genomes	Global	Study-wide	5008	T=0.206	C=0.794
1000Genomes	South Asian	Sub	978	T=0.250	C=0.750
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.257	C=0.743
The Genome Aggregation Database	African	Sub	8716	T=0.083	C=0.917
The Genome Aggregation Database	American	Sub	832	T=0.220	C=0.78,
The Genome Aggregation Database	East Asian	Sub	1610	T=0.347	C=0.653
The Genome Aggregation Database	Europe	Sub	18354	T=0.234	C=0.765
The Genome Aggregation Database	Global	Study-wide	29812	T=0.196	C=0.804
The Genome Aggregation Database	Other	Sub	300	T=0.260	C=0.74,
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.260	C=0.740

PMID	Title	Author	Journal
27488534	Novel Association of Genetic Markers Affecting CYP2A6 Activity and Lung Cancer Risk.	Patel YM	Cancer Res

P-Value

SNP ID	p-value	Traits	Study
rs4079366	8E-14	nicotine metabolite ratio in current smokers	27488534

eQTL of rs4079366 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 rs4079366 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	-36390
chr19	41310386	41310560	E067	-36208
chr19	41310588	41311205	E067	-35563
chr19	41311222	41311679	E067	-35089
chr19	41311756	41311846	E067	-34922
chr19	41311901	41311984	E067	-34784
chr19	41314057	41314164	E067	-32604
chr19	41314165	41314366	E067	-32402
chr19	41314383	41314438	E067	-32330
chr19	41314543	41314844	E067	-31924
chr19	41318614	41318775	E067	-27993
chr19	41318893	41318990	E067	-27778
chr19	41319058	41319424	E067	-27344
chr19	41319757	41319828	E067	-26940
chr19	41324139	41324179	E067	-22589
chr19	41324351	41324854	E067	-21914
chr19	41324907	41325135	E067	-21633
chr19	41325420	41326011	E067	-20757
chr19	41328596	41329263	E067	-17505
chr19	41333021	41333471	E067	-13297
chr19	41297251	41297337	E068	-49431
chr19	41297391	41298299	E068	-48469
chr19	41298323	41298444	E068	-48324
chr19	41298474	41298695	E068	-48073
chr19	41310386	41310560	E068	-36208
chr19	41310588	41311205	E068	-35563
chr19	41311222	41311679	E068	-35089
chr19	41311756	41311846	E068	-34922
chr19	41311901	41311984	E068	-34784
chr19	41313359	41314035	E068	-32733
chr19	41315417	41315497	E068	-31271
chr19	41315541	41315630	E068	-31138
chr19	41315675	41315793	E068	-30975
chr19	41318461	41318553	E068	-28215
chr19	41318614	41318775	E068	-27993
chr19	41318893	41318990	E068	-27778
chr19	41324907	41325135	E068	-21633
chr19	41325420	41326011	E068	-20757
chr19	41328596	41329263	E068	-17505
chr19	41333021	41333471	E068	-13297
chr19	41307265	41307523	E069	-39245
chr19	41310588	41311205	E069	-35563
chr19	41311222	41311679	E069	-35089
chr19	41311756	41311846	E069	-34922
chr19	41311901	41311984	E069	-34784
chr19	41313359	41314035	E069	-32733
chr19	41315171	41315349	E069	-31419
chr19	41315417	41315497	E069	-31271
chr19	41315541	41315630	E069	-31138
chr19	41315675	41315793	E069	-30975
chr19	41319058	41319424	E069	-27344
chr19	41319502	41319594	E069	-27174
chr19	41319632	41319711	E069	-27057
chr19	41323661	41323817	E069	-22951
chr19	41323901	41323956	E069	-22812
chr19	41324139	41324179	E069	-22589
chr19	41324351	41324854	E069	-21914
chr19	41324907	41325135	E069	-21633
chr19	41325420	41326011	E069	-20757
chr19	41328368	41328433	E069	-18335
chr19	41328596	41329263	E069	-17505
chr19	41311222	41311679	E070	-35089
chr19	41311756	41311846	E070	-34922
chr19	41311901	41311984	E070	-34784
chr19	41313359	41314035	E070	-32733
chr19	41314057	41314164	E070	-32604
chr19	41339246	41339303	E070	-7465
chr19	41309197	41310378	E071	-36390
chr19	41310386	41310560	E071	-36208
chr19	41310588	41311205	E071	-35563
chr19	41311222	41311679	E071	-35089
chr19	41311756	41311846	E071	-34922
chr19	41311901	41311984	E071	-34784
chr19	41313359	41314035	E071	-32733
chr19	41314057	41314164	E071	-32604
chr19	41314165	41314366	E071	-32402
chr19	41314383	41314438	E071	-32330
chr19	41314543	41314844	E071	-31924
chr19	41314849	41314965	E071	-31803
chr19	41315171	41315349	E071	-31419
chr19	41315417	41315497	E071	-31271
chr19	41315541	41315630	E071	-31138
chr19	41315675	41315793	E071	-30975
chr19	41318461	41318553	E071	-28215
chr19	41318614	41318775	E071	-27993
chr19	41318893	41318990	E071	-27778
chr19	41319058	41319424	E071	-27344
chr19	41319502	41319594	E071	-27174
chr19	41319632	41319711	E071	-27057
chr19	41319757	41319828	E071	-26940
chr19	41319892	41320080	E071	-26688
chr19	41324139	41324179	E071	-22589
chr19	41324351	41324854	E071	-21914
chr19	41324907	41325135	E071	-21633
chr19	41325420	41326011	E071	-20757
chr19	41328368	41328433	E071	-18335
chr19	41328596	41329263	E071	-17505
chr19	41329354	41329411	E071	-17357
chr19	41297251	41297337	E072	-49431
chr19	41309197	41310378	E072	-36390
chr19	41310386	41310560	E072	-36208
chr19	41310588	41311205	E072	-35563
chr19	41311222	41311679	E072	-35089
chr19	41311756	41311846	E072	-34922
chr19	41311901	41311984	E072	-34784
chr19	41313359	41314035	E072	-32733
chr19	41314057	41314164	E072	-32604
chr19	41314165	41314366	E072	-32402
chr19	41314383	41314438	E072	-32330
chr19	41314543	41314844	E072	-31924
chr19	41315541	41315630	E072	-31138
chr19	41315675	41315793	E072	-30975
chr19	41318461	41318553	E072	-28215
chr19	41324139	41324179	E072	-22589
chr19	41324907	41325135	E072	-21633
chr19	41328596	41329263	E072	-17505
chr19	41333021	41333471	E072	-13297
chr19	41339828	41339912	E072	-6856
chr19	41297391	41298299	E073	-48469
chr19	41298323	41298444	E073	-48324
chr19	41310588	41311205	E073	-35563
chr19	41311222	41311679	E073	-35089
chr19	41311756	41311846	E073	-34922
chr19	41311901	41311984	E073	-34784
chr19	41313359	41314035	E073	-32733
chr19	41318461	41318553	E073	-28215
chr19	41318614	41318775	E073	-27993
chr19	41318893	41318990	E073	-27778
chr19	41319058	41319424	E073	-27344
chr19	41324351	41324854	E073	-21914
chr19	41324907	41325135	E073	-21633
chr19	41328009	41328074	E073	-18694
chr19	41328217	41328302	E073	-18466
chr19	41328368	41328433	E073	-18335
chr19	41328596	41329263	E073	-17505
chr19	41333021	41333471	E073	-13297
chr19	41309197	41310378	E074	-36390
chr19	41310386	41310560	E074	-36208
chr19	41310588	41311205	E074	-35563
chr19	41311222	41311679	E074	-35089
chr19	41311756	41311846	E074	-34922
chr19	41311901	41311984	E074	-34784
chr19	41313359	41314035	E074	-32733
chr19	41314057	41314164	E074	-32604
chr19	41314165	41314366	E074	-32402
chr19	41314383	41314438	E074	-32330
chr19	41315541	41315630	E074	-31138
chr19	41315675	41315793	E074	-30975
chr19	41318461	41318553	E074	-28215
chr19	41318614	41318775	E074	-27993
chr19	41318893	41318990	E074	-27778
chr19	41319058	41319424	E074	-27344
chr19	41319502	41319594	E074	-27174
chr19	41319632	41319711	E074	-27057
chr19	41319757	41319828	E074	-26940
chr19	41319892	41320080	E074	-26688
chr19	41324139	41324179	E074	-22589
chr19	41324351	41324854	E074	-21914
chr19	41325420	41326011	E074	-20757
chr19	41328217	41328302	E074	-18466
chr19	41328368	41328433	E074	-18335
chr19	41328596	41329263	E074	-17505
chr19	41329354	41329411	E074	-17357
chr19	41333021	41333471	E074	-13297
chr19	41339246	41339303	E074	-7465
chr19	41339346	41339498	E074	-7270
chr19	41339828	41339912	E074	-6856
chr19	41354980	41355083	E074	8212
chr19	41306816	41307243	E081	-39525
chr19	41307265	41307523	E081	-39245
chr19	41309197	41310378	E081	-36390
chr19	41310386	41310560	E081	-36208
chr19	41310588	41311205	E081	-35563
chr19	41311222	41311679	E081	-35089
chr19	41311756	41311846	E081	-34922
chr19	41311901	41311984	E081	-34784
chr19	41312044	41313329	E081	-33439
chr19	41324351	41324854	E081	-21914
chr19	41311222	41311679	E082	-35089
chr19	41311756	41311846	E082	-34922
chr19	41311901	41311984	E082	-34784
chr19	41318461	41318553	E082	-28215
chr19	41318614	41318775	E082	-27993
chr19	41318893	41318990	E082	-27778
chr19	41323661	41323817	E082	-22951
chr19	41323901	41323956	E082	-22812
chr19	41324139	41324179	E082	-22589
chr19	41324351	41324854	E082	-21914

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	41303789	41306736	E067	-40032
chr19	41316570	41316987	E067	-29781
chr19	41317036	41317275	E067	-29493
chr19	41354337	41354458	E067	7569
chr19	41354484	41354854	E067	7716
chr19	41303789	41306736	E068	-40032
chr19	41316570	41316987	E068	-29781
chr19	41317036	41317275	E068	-29493
chr19	41303789	41306736	E069	-40032
chr19	41316570	41316987	E069	-29781
chr19	41317036	41317275	E069	-29493
chr19	41303789	41306736	E070	-40032
chr19	41316570	41316987	E070	-29781
chr19	41317036	41317275	E070	-29493
chr19	41354484	41354854	E070	7716
chr19	41303789	41306736	E071	-40032
chr19	41316570	41316987	E071	-29781
chr19	41317036	41317275	E071	-29493
chr19	41303789	41306736	E072	-40032
chr19	41316570	41316987	E072	-29781
chr19	41317036	41317275	E072	-29493
chr19	41354337	41354458	E072	7569
chr19	41354484	41354854	E072	7716
chr19	41303789	41306736	E073	-40032
chr19	41316570	41316987	E073	-29781
chr19	41317036	41317275	E073	-29493
chr19	41303789	41306736	E074	-40032
chr19	41316570	41316987	E074	-29781
chr19	41317036	41317275	E074	-29493
chr19	41303789	41306736	E082	-40032
chr19	41316570	41316987	E082	-29781
chr19	41317036	41317275	E082	-29493