rs12459249

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0343 (10234/29814,GnomAD)
T==0395 (1976/5008,1000G)
T==0332 (1279/3854,ALSPAC)
T==0336 (1246/3708,TWINSUK)

Position: chr19:40833991 (GRCh38.p7) (19q13.2)

Phenotype: ND

Dataset:

GWASCatalog

Publications: 2 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.40833991T>C
GRCh37.p13 chr 19	NC_000019.9:g.41339896T>C

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.328	C=0.672
1000Genomes	American	Sub	694	T=0.290	C=0.710
1000Genomes	East Asian	Sub	1008	T=0.543	C=0.457
1000Genomes	Europe	Sub	1006	T=0.318	C=0.682
1000Genomes	Global	Study-wide	5008	T=0.395	C=0.605
1000Genomes	South Asian	Sub	978	T=0.490	C=0.510
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.332	C=0.668
The Genome Aggregation Database	African	Sub	8642	T=0.341	C=0.659
The Genome Aggregation Database	American	Sub	836	T=0.320	C=0.680
The Genome Aggregation Database	East Asian	Sub	1608	T=0.572	C=0.428
The Genome Aggregation Database	Europe	Sub	18428	T=0.326	C=0.673
The Genome Aggregation Database	Global	Study-wide	29814	T=0.343	C=0.656
The Genome Aggregation Database	Other	Sub	300	T=0.280	C=0.720
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.336	C=0.664

PMID	Title	Author	Journal
28921760	Genome-wide association study of a nicotine metabolism biomarker in African American smokers: impact of chromosome 19 genetic influences.	Chenoweth MJ	Addiction
27113016	Genome-Wide Association of the Laboratory-Based Nicotine Metabolite Ratio in Three Ancestries.	Baurley JW	Nicotine Tob Res

P-Value

SNP ID	p-value	Traits	Study
rs12459249	1E-39	nicotine metabolite ratio in current smokers	28921760

eQTL of rs12459249 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:41339896	CYP2G1P	ENSG00000130612.10	T>C	2.1788e-2	-56835	Cerebellum

meQTL of rs12459249 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	-29518
chr19	41310386	41310560	E067	-29336
chr19	41310588	41311205	E067	-28691
chr19	41311222	41311679	E067	-28217
chr19	41311756	41311846	E067	-28050
chr19	41311901	41311984	E067	-27912
chr19	41314057	41314164	E067	-25732
chr19	41314165	41314366	E067	-25530
chr19	41314383	41314438	E067	-25458
chr19	41314543	41314844	E067	-25052
chr19	41318614	41318775	E067	-21121
chr19	41318893	41318990	E067	-20906
chr19	41319058	41319424	E067	-20472
chr19	41319757	41319828	E067	-20068
chr19	41324139	41324179	E067	-15717
chr19	41324351	41324854	E067	-15042
chr19	41324907	41325135	E067	-14761
chr19	41325420	41326011	E067	-13885
chr19	41328596	41329263	E067	-10633
chr19	41333021	41333471	E067	-6425
chr19	41297251	41297337	E068	-42559
chr19	41297391	41298299	E068	-41597
chr19	41298323	41298444	E068	-41452
chr19	41298474	41298695	E068	-41201
chr19	41310386	41310560	E068	-29336
chr19	41310588	41311205	E068	-28691
chr19	41311222	41311679	E068	-28217
chr19	41311756	41311846	E068	-28050
chr19	41311901	41311984	E068	-27912
chr19	41313359	41314035	E068	-25861
chr19	41315417	41315497	E068	-24399
chr19	41315541	41315630	E068	-24266
chr19	41315675	41315793	E068	-24103
chr19	41318461	41318553	E068	-21343
chr19	41318614	41318775	E068	-21121
chr19	41318893	41318990	E068	-20906
chr19	41324907	41325135	E068	-14761
chr19	41325420	41326011	E068	-13885
chr19	41328596	41329263	E068	-10633
chr19	41333021	41333471	E068	-6425
chr19	41307265	41307523	E069	-32373
chr19	41310588	41311205	E069	-28691
chr19	41311222	41311679	E069	-28217
chr19	41311756	41311846	E069	-28050
chr19	41311901	41311984	E069	-27912
chr19	41313359	41314035	E069	-25861
chr19	41315171	41315349	E069	-24547
chr19	41315417	41315497	E069	-24399
chr19	41315541	41315630	E069	-24266
chr19	41315675	41315793	E069	-24103
chr19	41319058	41319424	E069	-20472
chr19	41319502	41319594	E069	-20302
chr19	41319632	41319711	E069	-20185
chr19	41323661	41323817	E069	-16079
chr19	41323901	41323956	E069	-15940
chr19	41324139	41324179	E069	-15717
chr19	41324351	41324854	E069	-15042
chr19	41324907	41325135	E069	-14761
chr19	41325420	41326011	E069	-13885
chr19	41328368	41328433	E069	-11463
chr19	41328596	41329263	E069	-10633
chr19	41311222	41311679	E070	-28217
chr19	41311756	41311846	E070	-28050
chr19	41311901	41311984	E070	-27912
chr19	41313359	41314035	E070	-25861
chr19	41314057	41314164	E070	-25732
chr19	41339246	41339303	E070	-593
chr19	41309197	41310378	E071	-29518
chr19	41310386	41310560	E071	-29336
chr19	41310588	41311205	E071	-28691
chr19	41311222	41311679	E071	-28217
chr19	41311756	41311846	E071	-28050
chr19	41311901	41311984	E071	-27912
chr19	41313359	41314035	E071	-25861
chr19	41314057	41314164	E071	-25732
chr19	41314165	41314366	E071	-25530
chr19	41314383	41314438	E071	-25458
chr19	41314543	41314844	E071	-25052
chr19	41314849	41314965	E071	-24931
chr19	41315171	41315349	E071	-24547
chr19	41315417	41315497	E071	-24399
chr19	41315541	41315630	E071	-24266
chr19	41315675	41315793	E071	-24103
chr19	41318461	41318553	E071	-21343
chr19	41318614	41318775	E071	-21121
chr19	41318893	41318990	E071	-20906
chr19	41319058	41319424	E071	-20472
chr19	41319502	41319594	E071	-20302
chr19	41319632	41319711	E071	-20185
chr19	41319757	41319828	E071	-20068
chr19	41319892	41320080	E071	-19816
chr19	41324139	41324179	E071	-15717
chr19	41324351	41324854	E071	-15042
chr19	41324907	41325135	E071	-14761
chr19	41325420	41326011	E071	-13885
chr19	41328368	41328433	E071	-11463
chr19	41328596	41329263	E071	-10633
chr19	41329354	41329411	E071	-10485
chr19	41297251	41297337	E072	-42559
chr19	41309197	41310378	E072	-29518
chr19	41310386	41310560	E072	-29336
chr19	41310588	41311205	E072	-28691
chr19	41311222	41311679	E072	-28217
chr19	41311756	41311846	E072	-28050
chr19	41311901	41311984	E072	-27912
chr19	41313359	41314035	E072	-25861
chr19	41314057	41314164	E072	-25732
chr19	41314165	41314366	E072	-25530
chr19	41314383	41314438	E072	-25458
chr19	41314543	41314844	E072	-25052
chr19	41315541	41315630	E072	-24266
chr19	41315675	41315793	E072	-24103
chr19	41318461	41318553	E072	-21343
chr19	41324139	41324179	E072	-15717
chr19	41324907	41325135	E072	-14761
chr19	41328596	41329263	E072	-10633
chr19	41333021	41333471	E072	-6425
chr19	41339828	41339912	E072	0
chr19	41297391	41298299	E073	-41597
chr19	41298323	41298444	E073	-41452
chr19	41310588	41311205	E073	-28691
chr19	41311222	41311679	E073	-28217
chr19	41311756	41311846	E073	-28050
chr19	41311901	41311984	E073	-27912
chr19	41313359	41314035	E073	-25861
chr19	41318461	41318553	E073	-21343
chr19	41318614	41318775	E073	-21121
chr19	41318893	41318990	E073	-20906
chr19	41319058	41319424	E073	-20472
chr19	41324351	41324854	E073	-15042
chr19	41324907	41325135	E073	-14761
chr19	41328009	41328074	E073	-11822
chr19	41328217	41328302	E073	-11594
chr19	41328368	41328433	E073	-11463
chr19	41328596	41329263	E073	-10633
chr19	41333021	41333471	E073	-6425
chr19	41309197	41310378	E074	-29518
chr19	41310386	41310560	E074	-29336
chr19	41310588	41311205	E074	-28691
chr19	41311222	41311679	E074	-28217
chr19	41311756	41311846	E074	-28050
chr19	41311901	41311984	E074	-27912
chr19	41313359	41314035	E074	-25861
chr19	41314057	41314164	E074	-25732
chr19	41314165	41314366	E074	-25530
chr19	41314383	41314438	E074	-25458
chr19	41315541	41315630	E074	-24266
chr19	41315675	41315793	E074	-24103
chr19	41318461	41318553	E074	-21343
chr19	41318614	41318775	E074	-21121
chr19	41318893	41318990	E074	-20906
chr19	41319058	41319424	E074	-20472
chr19	41319502	41319594	E074	-20302
chr19	41319632	41319711	E074	-20185
chr19	41319757	41319828	E074	-20068
chr19	41319892	41320080	E074	-19816
chr19	41324139	41324179	E074	-15717
chr19	41324351	41324854	E074	-15042
chr19	41325420	41326011	E074	-13885
chr19	41328217	41328302	E074	-11594
chr19	41328368	41328433	E074	-11463
chr19	41328596	41329263	E074	-10633
chr19	41329354	41329411	E074	-10485
chr19	41333021	41333471	E074	-6425
chr19	41339246	41339303	E074	-593
chr19	41339346	41339498	E074	-398
chr19	41339828	41339912	E074	0
chr19	41354980	41355083	E074	15084
chr19	41306816	41307243	E081	-32653
chr19	41307265	41307523	E081	-32373
chr19	41309197	41310378	E081	-29518
chr19	41310386	41310560	E081	-29336
chr19	41310588	41311205	E081	-28691
chr19	41311222	41311679	E081	-28217
chr19	41311756	41311846	E081	-28050
chr19	41311901	41311984	E081	-27912
chr19	41312044	41313329	E081	-26567
chr19	41324351	41324854	E081	-15042
chr19	41311222	41311679	E082	-28217
chr19	41311756	41311846	E082	-28050
chr19	41311901	41311984	E082	-27912
chr19	41318461	41318553	E082	-21343
chr19	41318614	41318775	E082	-21121
chr19	41318893	41318990	E082	-20906
chr19	41323661	41323817	E082	-16079
chr19	41323901	41323956	E082	-15940
chr19	41324139	41324179	E082	-15717
chr19	41324351	41324854	E082	-15042

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	41303789	41306736	E067	-33160
chr19	41316570	41316987	E067	-22909
chr19	41317036	41317275	E067	-22621
chr19	41354337	41354458	E067	14441
chr19	41354484	41354854	E067	14588
chr19	41303789	41306736	E068	-33160
chr19	41316570	41316987	E068	-22909
chr19	41317036	41317275	E068	-22621
chr19	41303789	41306736	E069	-33160
chr19	41316570	41316987	E069	-22909
chr19	41317036	41317275	E069	-22621
chr19	41303789	41306736	E070	-33160
chr19	41316570	41316987	E070	-22909
chr19	41317036	41317275	E070	-22621
chr19	41354484	41354854	E070	14588
chr19	41303789	41306736	E071	-33160
chr19	41316570	41316987	E071	-22909
chr19	41317036	41317275	E071	-22621
chr19	41303789	41306736	E072	-33160
chr19	41316570	41316987	E072	-22909
chr19	41317036	41317275	E072	-22621
chr19	41354337	41354458	E072	14441
chr19	41354484	41354854	E072	14588
chr19	41303789	41306736	E073	-33160
chr19	41316570	41316987	E073	-22909
chr19	41317036	41317275	E073	-22621
chr19	41303789	41306736	E074	-33160
chr19	41316570	41316987	E074	-22909
chr19	41317036	41317275	E074	-22621
chr19	41303789	41306736	E082	-33160
chr19	41316570	41316987	E082	-22909
chr19	41317036	41317275	E082	-22621