rs11878604

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0154 (4533/29348,GnomAD)
C=0152 (4431/29118,TOPMED)
C=0219 (1097/5008,1000G)
C=0066 (256/3854,ALSPAC)
C=0074 (276/3708,TWINSUK)

Position: chr19:40827379 (GRCh38.p7) (19q13.2)

Phenotype: ND

Dataset:

GWASCatalog

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 192 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.40827379T>C
GRCh37.p13 chr 19	NC_000019.9:g.41333284T>C

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.750	C=0.250
1000Genomes	American	Sub	694	T=0.870	C=0.130
1000Genomes	East Asian	Sub	1008	T=0.617	C=0.383
1000Genomes	Europe	Sub	1006	T=0.916	C=0.084
1000Genomes	Global	Study-wide	5008	T=0.781	C=0.219
1000Genomes	South Asian	Sub	978	T=0.790	C=0.210
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.934	C=0.066
The Genome Aggregation Database	African	Sub	8212	T=0.747	C=0.253
The Genome Aggregation Database	American	Sub	832	T=0.850	C=0.150
The Genome Aggregation Database	East Asian	Sub	1604	T=0.622	C=0.378
The Genome Aggregation Database	Europe	Sub	18398	T=0.907	C=0.092
The Genome Aggregation Database	Global	Study-wide	29348	T=0.845	C=0.154
The Genome Aggregation Database	Other	Sub	302	T=0.910	C=0.090
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.847	C=0.152
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.926	C=0.074

PMID	Title	Author	Journal
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
rs11878604	7E-24	nicotine metabolite ratio in current smokers	27488534

eQTL of rs11878604 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 rs11878604 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	-22906
chr19	41310386	41310560	E067	-22724
chr19	41310588	41311205	E067	-22079
chr19	41311222	41311679	E067	-21605
chr19	41311756	41311846	E067	-21438
chr19	41311901	41311984	E067	-21300
chr19	41314057	41314164	E067	-19120
chr19	41314165	41314366	E067	-18918
chr19	41314383	41314438	E067	-18846
chr19	41314543	41314844	E067	-18440
chr19	41318614	41318775	E067	-14509
chr19	41318893	41318990	E067	-14294
chr19	41319058	41319424	E067	-13860
chr19	41319757	41319828	E067	-13456
chr19	41324139	41324179	E067	-9105
chr19	41324351	41324854	E067	-8430
chr19	41324907	41325135	E067	-8149
chr19	41325420	41326011	E067	-7273
chr19	41328596	41329263	E067	-4021
chr19	41333021	41333471	E067	0
chr19	41297251	41297337	E068	-35947
chr19	41297391	41298299	E068	-34985
chr19	41298323	41298444	E068	-34840
chr19	41298474	41298695	E068	-34589
chr19	41310386	41310560	E068	-22724
chr19	41310588	41311205	E068	-22079
chr19	41311222	41311679	E068	-21605
chr19	41311756	41311846	E068	-21438
chr19	41311901	41311984	E068	-21300
chr19	41313359	41314035	E068	-19249
chr19	41315417	41315497	E068	-17787
chr19	41315541	41315630	E068	-17654
chr19	41315675	41315793	E068	-17491
chr19	41318461	41318553	E068	-14731
chr19	41318614	41318775	E068	-14509
chr19	41318893	41318990	E068	-14294
chr19	41324907	41325135	E068	-8149
chr19	41325420	41326011	E068	-7273
chr19	41328596	41329263	E068	-4021
chr19	41333021	41333471	E068	0
chr19	41307265	41307523	E069	-25761
chr19	41310588	41311205	E069	-22079
chr19	41311222	41311679	E069	-21605
chr19	41311756	41311846	E069	-21438
chr19	41311901	41311984	E069	-21300
chr19	41313359	41314035	E069	-19249
chr19	41315171	41315349	E069	-17935
chr19	41315417	41315497	E069	-17787
chr19	41315541	41315630	E069	-17654
chr19	41315675	41315793	E069	-17491
chr19	41319058	41319424	E069	-13860
chr19	41319502	41319594	E069	-13690
chr19	41319632	41319711	E069	-13573
chr19	41323661	41323817	E069	-9467
chr19	41323901	41323956	E069	-9328
chr19	41324139	41324179	E069	-9105
chr19	41324351	41324854	E069	-8430
chr19	41324907	41325135	E069	-8149
chr19	41325420	41326011	E069	-7273
chr19	41328368	41328433	E069	-4851
chr19	41328596	41329263	E069	-4021
chr19	41311222	41311679	E070	-21605
chr19	41311756	41311846	E070	-21438
chr19	41311901	41311984	E070	-21300
chr19	41313359	41314035	E070	-19249
chr19	41314057	41314164	E070	-19120
chr19	41339246	41339303	E070	5962
chr19	41309197	41310378	E071	-22906
chr19	41310386	41310560	E071	-22724
chr19	41310588	41311205	E071	-22079
chr19	41311222	41311679	E071	-21605
chr19	41311756	41311846	E071	-21438
chr19	41311901	41311984	E071	-21300
chr19	41313359	41314035	E071	-19249
chr19	41314057	41314164	E071	-19120
chr19	41314165	41314366	E071	-18918
chr19	41314383	41314438	E071	-18846
chr19	41314543	41314844	E071	-18440
chr19	41314849	41314965	E071	-18319
chr19	41315171	41315349	E071	-17935
chr19	41315417	41315497	E071	-17787
chr19	41315541	41315630	E071	-17654
chr19	41315675	41315793	E071	-17491
chr19	41318461	41318553	E071	-14731
chr19	41318614	41318775	E071	-14509
chr19	41318893	41318990	E071	-14294
chr19	41319058	41319424	E071	-13860
chr19	41319502	41319594	E071	-13690
chr19	41319632	41319711	E071	-13573
chr19	41319757	41319828	E071	-13456
chr19	41319892	41320080	E071	-13204
chr19	41324139	41324179	E071	-9105
chr19	41324351	41324854	E071	-8430
chr19	41324907	41325135	E071	-8149
chr19	41325420	41326011	E071	-7273
chr19	41328368	41328433	E071	-4851
chr19	41328596	41329263	E071	-4021
chr19	41329354	41329411	E071	-3873
chr19	41285641	41285695	E072	-47589
chr19	41285796	41285841	E072	-47443
chr19	41285887	41286023	E072	-47261
chr19	41286106	41286207	E072	-47077
chr19	41297251	41297337	E072	-35947
chr19	41309197	41310378	E072	-22906
chr19	41310386	41310560	E072	-22724
chr19	41310588	41311205	E072	-22079
chr19	41311222	41311679	E072	-21605
chr19	41311756	41311846	E072	-21438
chr19	41311901	41311984	E072	-21300
chr19	41313359	41314035	E072	-19249
chr19	41314057	41314164	E072	-19120
chr19	41314165	41314366	E072	-18918
chr19	41314383	41314438	E072	-18846
chr19	41314543	41314844	E072	-18440
chr19	41315541	41315630	E072	-17654
chr19	41315675	41315793	E072	-17491
chr19	41318461	41318553	E072	-14731
chr19	41324139	41324179	E072	-9105
chr19	41324907	41325135	E072	-8149
chr19	41328596	41329263	E072	-4021
chr19	41333021	41333471	E072	0
chr19	41339828	41339912	E072	6544
chr19	41297391	41298299	E073	-34985
chr19	41298323	41298444	E073	-34840
chr19	41310588	41311205	E073	-22079
chr19	41311222	41311679	E073	-21605
chr19	41311756	41311846	E073	-21438
chr19	41311901	41311984	E073	-21300
chr19	41313359	41314035	E073	-19249
chr19	41318461	41318553	E073	-14731
chr19	41318614	41318775	E073	-14509
chr19	41318893	41318990	E073	-14294
chr19	41319058	41319424	E073	-13860
chr19	41324351	41324854	E073	-8430
chr19	41324907	41325135	E073	-8149
chr19	41328009	41328074	E073	-5210
chr19	41328217	41328302	E073	-4982
chr19	41328368	41328433	E073	-4851
chr19	41328596	41329263	E073	-4021
chr19	41333021	41333471	E073	0
chr19	41309197	41310378	E074	-22906
chr19	41310386	41310560	E074	-22724
chr19	41310588	41311205	E074	-22079
chr19	41311222	41311679	E074	-21605
chr19	41311756	41311846	E074	-21438
chr19	41311901	41311984	E074	-21300
chr19	41313359	41314035	E074	-19249
chr19	41314057	41314164	E074	-19120
chr19	41314165	41314366	E074	-18918
chr19	41314383	41314438	E074	-18846
chr19	41315541	41315630	E074	-17654
chr19	41315675	41315793	E074	-17491
chr19	41318461	41318553	E074	-14731
chr19	41318614	41318775	E074	-14509
chr19	41318893	41318990	E074	-14294
chr19	41319058	41319424	E074	-13860
chr19	41319502	41319594	E074	-13690
chr19	41319632	41319711	E074	-13573
chr19	41319757	41319828	E074	-13456
chr19	41319892	41320080	E074	-13204
chr19	41324139	41324179	E074	-9105
chr19	41324351	41324854	E074	-8430
chr19	41325420	41326011	E074	-7273
chr19	41328217	41328302	E074	-4982
chr19	41328368	41328433	E074	-4851
chr19	41328596	41329263	E074	-4021
chr19	41329354	41329411	E074	-3873
chr19	41333021	41333471	E074	0
chr19	41339246	41339303	E074	5962
chr19	41339346	41339498	E074	6062
chr19	41339828	41339912	E074	6544
chr19	41354980	41355083	E074	21696
chr19	41306816	41307243	E081	-26041
chr19	41307265	41307523	E081	-25761
chr19	41309197	41310378	E081	-22906
chr19	41310386	41310560	E081	-22724
chr19	41310588	41311205	E081	-22079
chr19	41311222	41311679	E081	-21605
chr19	41311756	41311846	E081	-21438
chr19	41311901	41311984	E081	-21300
chr19	41312044	41313329	E081	-19955
chr19	41324351	41324854	E081	-8430
chr19	41311222	41311679	E082	-21605
chr19	41311756	41311846	E082	-21438
chr19	41311901	41311984	E082	-21300
chr19	41318461	41318553	E082	-14731
chr19	41318614	41318775	E082	-14509
chr19	41318893	41318990	E082	-14294
chr19	41323661	41323817	E082	-9467
chr19	41323901	41323956	E082	-9328
chr19	41324139	41324179	E082	-9105
chr19	41324351	41324854	E082	-8430

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	41303789	41306736	E067	-26548
chr19	41316570	41316987	E067	-16297
chr19	41317036	41317275	E067	-16009
chr19	41354337	41354458	E067	21053
chr19	41354484	41354854	E067	21200
chr19	41303789	41306736	E068	-26548
chr19	41316570	41316987	E068	-16297
chr19	41317036	41317275	E068	-16009
chr19	41303789	41306736	E069	-26548
chr19	41316570	41316987	E069	-16297
chr19	41317036	41317275	E069	-16009
chr19	41303789	41306736	E070	-26548
chr19	41316570	41316987	E070	-16297
chr19	41317036	41317275	E070	-16009
chr19	41354484	41354854	E070	21200
chr19	41303789	41306736	E071	-26548
chr19	41316570	41316987	E071	-16297
chr19	41317036	41317275	E071	-16009
chr19	41303789	41306736	E072	-26548
chr19	41316570	41316987	E072	-16297
chr19	41317036	41317275	E072	-16009
chr19	41354337	41354458	E072	21053
chr19	41354484	41354854	E072	21200
chr19	41303789	41306736	E073	-26548
chr19	41316570	41316987	E073	-16297
chr19	41317036	41317275	E073	-16009
chr19	41303789	41306736	E074	-26548
chr19	41316570	41316987	E074	-16297
chr19	41317036	41317275	E074	-16009
chr19	41303789	41306736	E082	-26548
chr19	41316570	41316987	E082	-16297
chr19	41317036	41317275	E082	-16009