rs2072661

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CHRNB2 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0251 (7524/29888,GnomAD)
A=0266 (7746/29118,TOPMED)
A=0265 (1325/5008,1000G)
A=0244 (940/3854,ALSPAC)
A=0233 (864/3708,TWINSUK)

Position: chr1:154576404 (GRCh38.p7) (1q21.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 24 publication(s)

Genomic View: See rs on genome

Enhancer: 168 Enhancers around

Promoter: 53 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.154576404G>A
GRCh37.p13 chr 1	NC_000001.10:g.154548880G>A
CHRNB2 RefSeqGene	NG_008027.1:g.13624G>A

Gene: CHRNB2, cholinergic receptor nicotinic beta 2 subunit(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CHRNB2 transcript	NM_000748.2:c.	N/A	3 Prime UTR Variant
CHRNB2 transcript variant X2	XM_017000180.1:c.	N/A	3 Prime UTR Variant
CHRNB2 transcript variant X1	XR_001736952.1:n....XR_001736952.1:n.2233G>A	G>A	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.718	A=0.282
1000Genomes	American	Sub	694	G=0.760	A=0.240
1000Genomes	East Asian	Sub	1008	G=0.683	A=0.317
1000Genomes	Europe	Sub	1006	G=0.733	A=0.267
1000Genomes	Global	Study-wide	5008	G=0.735	A=0.265
1000Genomes	South Asian	Sub	978	G=0.800	A=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.756	A=0.244
The Genome Aggregation Database	African	Sub	8704	G=0.726	A=0.274
The Genome Aggregation Database	American	Sub	838	G=0.760	A=0.240
The Genome Aggregation Database	East Asian	Sub	1612	G=0.725	A=0.275
The Genome Aggregation Database	Europe	Sub	18432	G=0.760	A=0.240
The Genome Aggregation Database	Global	Study-wide	29888	G=0.748	A=0.251
The Genome Aggregation Database	Other	Sub	302	G=0.760	A=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.734	A=0.266
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.767	A=0.233

PMID	Title	Author	Journal
20981002	Breaking barriers in the genomics and pharmacogenetics of drug addiction.	Ho MK	Clin Pharmacol Ther
25819021	A review of pharmacogenetic studies of substance-related disorders.	Jones JD	Drug Alcohol Depend
19859904	Association and interaction analysis of variants in CHRNA5/CHRNA3/CHRNB4 gene cluster with nicotine dependence in African and European Americans.	Li MD	Am J Med Genet B Neuropsychiatr Genet
21606948	Varenicline for smoking cessation: nausea severity and variation in nicotinic receptor genes.	Swan GE	Pharmacogenomics J
22180580	Association between nicotinic acetylcholine receptor single nucleotide polymorphisms and smoking cessation.	Spruell T	Nicotine Tob Res
21808284	Gender-stratified gene and gene-treatment interactions in smoking cessation.	Lee W	Pharmacogenomics J
20854418	CHRNB2 promoter region: association with subjective effects to nicotine and gene expression differences.	Hoft NR	Genes Brain Behav
18165968	Identification of pharmacogenetic markers in smoking cessation therapy.	Heitjan DF	Am J Med Genet B Neuropsychiatr Genet
22992668	Pharmacogenomics knowledge for personalized medicine.	Whirl-Carrillo M	Clin Pharmacol Ther
22103610	Biomarkers to optimize the treatment of nicotine dependence.	Schnoll RA	Biomark Med
18593715	Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessation.	Conti DV	Hum Mol Genet
17503330	A generalized combinatorial approach for detecting gene-by-gene and gene-by-environment interactions with application to nicotine dependence.	Lou XY	Am J Hum Genet
19482438	Association of genes coding for the alpha-4, alpha-5, beta-2 and beta-3 subunits of nicotinic receptors with cigarette smoking and nicotine dependence.	Etter JF	Addict Behav
22290489	Pharmacogenetics of smoking cessation: role of nicotine target and metabolism genes.	Gold AB	Hum Genet
19755656	Nicotinic acetylcholine receptor beta2 subunit (CHRNB2) gene and short-term ability to quit smoking in response to nicotine patch.	Perkins KA	Cancer Epidemiol Biomarkers Prev
23943838	Effect of neuronal nicotinic acetylcholine receptor genes (CHRN) on longitudinal cigarettes per day in adolescents and young adults.	Cannon DS	Nicotine Tob Res
19238175	New insights into the genetics of addiction.	Li MD	Nat Rev Genet
23691092	Associations of prenatal nicotine exposure and the dopamine related genes ANKK1 and DRD2 to verbal language.	Eicher JD	PLoS One
15154117	A common haplotype of the nicotine acetylcholine receptor alpha 4 subunit gene is associated with vulnerability to nicotine addiction in men.	Feng Y	Am J Hum Genet
25036316	Joint association of nicotinic acetylcholine receptor variants with abdominal obesity in American Indians: the Strong Heart Family Study.	Zhu Y	PLoS One
18534558	Gene-gene interactions among CHRNA4, CHRNB2, BDNF, and NTRK2 in nicotine dependence.	Li MD	Biol Psychiatry
20736995	Resequencing of nicotinic acetylcholine receptor genes and association of common and rare variants with the Fagerstrom test for nicotine dependence.	Wessel J	Neuropsychopharmacology
23249876	Nicotinic acetylcholine receptor variation and response to smoking cessation therapies.	Bergen AW	Pharmacogenet Genomics
24667010	Nicotine dependence as a moderator of genetic influences on smoking cessation treatment outcome.	Leventhal AM	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs2072661	0.001	Drug response to nicotine	18593715

eQTL of rs2072661 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 rs2072661 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 )
chr1	154521866	154521945	E067	-26935
chr1	154528861	154528935	E067	-19945
chr1	154545464	154545535	E067	-3345
chr1	154547223	154547709	E067	-1171
chr1	154548188	154548299	E067	-581
chr1	154571132	154571191	E067	22252
chr1	154571213	154571317	E067	22333
chr1	154571498	154571686	E067	22618
chr1	154571822	154571943	E067	22942
chr1	154572135	154572402	E067	23255
chr1	154573922	154573982	E067	25042
chr1	154574435	154574495	E067	25555
chr1	154574698	154574808	E067	25818
chr1	154575038	154575095	E067	26158
chr1	154575210	154575296	E067	26330
chr1	154575690	154575750	E067	26810
chr1	154575954	154576088	E067	27074
chr1	154578070	154578136	E067	29190
chr1	154583595	154583936	E067	34715
chr1	154584036	154584434	E067	35156
chr1	154587499	154587600	E067	38619
chr1	154587718	154587798	E067	38838
chr1	154597254	154597556	E067	48374
chr1	154597672	154597925	E067	48792
chr1	154528861	154528935	E068	-19945
chr1	154547223	154547709	E068	-1171
chr1	154549806	154549886	E068	926
chr1	154550243	154550287	E068	1363
chr1	154550288	154550342	E068	1408
chr1	154550423	154550968	E068	1543
chr1	154551162	154551212	E068	2282
chr1	154551242	154551315	E068	2362
chr1	154571132	154571191	E068	22252
chr1	154571213	154571317	E068	22333
chr1	154571498	154571686	E068	22618
chr1	154571822	154571943	E068	22942
chr1	154573922	154573982	E068	25042
chr1	154574435	154574495	E068	25555
chr1	154574698	154574808	E068	25818
chr1	154575038	154575095	E068	26158
chr1	154575210	154575296	E068	26330
chr1	154575690	154575750	E068	26810
chr1	154575954	154576088	E068	27074
chr1	154577436	154577476	E068	28556
chr1	154577515	154577778	E068	28635
chr1	154578070	154578136	E068	29190
chr1	154578542	154578592	E068	29662
chr1	154583421	154583522	E068	34541
chr1	154583595	154583936	E068	34715
chr1	154584036	154584434	E068	35156
chr1	154597672	154597925	E068	48792
chr1	154528861	154528935	E069	-19945
chr1	154547223	154547709	E069	-1171
chr1	154571132	154571191	E069	22252
chr1	154571213	154571317	E069	22333
chr1	154571498	154571686	E069	22618
chr1	154571822	154571943	E069	22942
chr1	154572135	154572402	E069	23255
chr1	154573922	154573982	E069	25042
chr1	154575954	154576088	E069	27074
chr1	154577436	154577476	E069	28556
chr1	154577515	154577778	E069	28635
chr1	154578070	154578136	E069	29190
chr1	154583421	154583522	E069	34541
chr1	154583595	154583936	E069	34715
chr1	154584036	154584434	E069	35156
chr1	154520456	154520816	E070	-28064
chr1	154520868	154521008	E070	-27872
chr1	154521117	154521271	E070	-27609
chr1	154521866	154521945	E070	-26935
chr1	154522655	154522853	E070	-26027
chr1	154545464	154545535	E070	-3345
chr1	154545661	154545711	E070	-3169
chr1	154545878	154545938	E070	-2942
chr1	154547223	154547709	E070	-1171
chr1	154548188	154548299	E070	-581
chr1	154548801	154548863	E070	-17
chr1	154588148	154588203	E070	39268
chr1	154588435	154588895	E070	39555
chr1	154528861	154528935	E071	-19945
chr1	154547223	154547709	E071	-1171
chr1	154571132	154571191	E071	22252
chr1	154571213	154571317	E071	22333
chr1	154571498	154571686	E071	22618
chr1	154571822	154571943	E071	22942
chr1	154572135	154572402	E071	23255
chr1	154573922	154573982	E071	25042
chr1	154574435	154574495	E071	25555
chr1	154574698	154574808	E071	25818
chr1	154575038	154575095	E071	26158
chr1	154575210	154575296	E071	26330
chr1	154575690	154575750	E071	26810
chr1	154575954	154576088	E071	27074
chr1	154578070	154578136	E071	29190
chr1	154578542	154578592	E071	29662
chr1	154583595	154583936	E071	34715
chr1	154584036	154584434	E071	35156
chr1	154589512	154589793	E071	40632
chr1	154597672	154597925	E071	48792
chr1	154521866	154521945	E072	-26935
chr1	154522655	154522853	E072	-26027
chr1	154528861	154528935	E072	-19945
chr1	154548188	154548299	E072	-581
chr1	154548801	154548863	E072	-17
chr1	154549806	154549886	E072	926
chr1	154571132	154571191	E072	22252
chr1	154571213	154571317	E072	22333
chr1	154571498	154571686	E072	22618
chr1	154571822	154571943	E072	22942
chr1	154572135	154572402	E072	23255
chr1	154578070	154578136	E072	29190
chr1	154583421	154583522	E072	34541
chr1	154584036	154584434	E072	35156
chr1	154594713	154594763	E072	45833
chr1	154595076	154595297	E072	46196
chr1	154521117	154521271	E073	-27609
chr1	154528317	154528371	E073	-20509
chr1	154547223	154547709	E073	-1171
chr1	154548188	154548299	E073	-581
chr1	154549806	154549886	E073	926
chr1	154550243	154550287	E073	1363
chr1	154550288	154550342	E073	1408
chr1	154550423	154550968	E073	1543
chr1	154571213	154571317	E073	22333
chr1	154571498	154571686	E073	22618
chr1	154571822	154571943	E073	22942
chr1	154572135	154572402	E073	23255
chr1	154575038	154575095	E073	26158
chr1	154575210	154575296	E073	26330
chr1	154575954	154576088	E073	27074
chr1	154577436	154577476	E073	28556
chr1	154577515	154577778	E073	28635
chr1	154578070	154578136	E073	29190
chr1	154587499	154587600	E073	38619
chr1	154587718	154587798	E073	38838
chr1	154587879	154587949	E073	38999
chr1	154528861	154528935	E074	-19945
chr1	154547223	154547709	E074	-1171
chr1	154571132	154571191	E074	22252
chr1	154571213	154571317	E074	22333
chr1	154571498	154571686	E074	22618
chr1	154571822	154571943	E074	22942
chr1	154572135	154572402	E074	23255
chr1	154573922	154573982	E074	25042
chr1	154574435	154574495	E074	25555
chr1	154577436	154577476	E074	28556
chr1	154577515	154577778	E074	28635
chr1	154578070	154578136	E074	29190
chr1	154578542	154578592	E074	29662
chr1	154583595	154583936	E074	34715
chr1	154584036	154584434	E074	35156
chr1	154521866	154521945	E081	-26935
chr1	154528861	154528935	E081	-19945
chr1	154547223	154547709	E081	-1171
chr1	154572135	154572402	E081	23255
chr1	154594512	154594663	E081	45632
chr1	154597672	154597925	E081	48792
chr1	154521117	154521271	E082	-27609
chr1	154521866	154521945	E082	-26935
chr1	154547223	154547709	E082	-1171
chr1	154548188	154548299	E082	-581
chr1	154584036	154584434	E082	35156
chr1	154594512	154594663	E082	45632
chr1	154594713	154594763	E082	45833
chr1	154594814	154594916	E082	45934
chr1	154595076	154595297	E082	46196
chr1	154595622	154595672	E082	46742
chr1	154595964	154596078	E082	47084

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	154530171	154530966	E067	-17914
chr1	154531000	154532537	E067	-16343
chr1	154539789	154539919	E067	-8961
chr1	154539954	154540863	E067	-8017
chr1	154579586	154582633	E067	30706
chr1	154530171	154530966	E068	-17914
chr1	154531000	154532537	E068	-16343
chr1	154539954	154540863	E068	-8017
chr1	154579586	154582633	E068	30706
chr1	154530171	154530966	E069	-17914
chr1	154531000	154532537	E069	-16343
chr1	154539711	154539765	E069	-9115
chr1	154539789	154539919	E069	-8961
chr1	154539954	154540863	E069	-8017
chr1	154579586	154582633	E069	30706
chr1	154530171	154530966	E070	-17914
chr1	154531000	154532537	E070	-16343
chr1	154539711	154539765	E070	-9115
chr1	154539789	154539919	E070	-8961
chr1	154539954	154540863	E070	-8017
chr1	154579586	154582633	E070	30706
chr1	154530171	154530966	E071	-17914
chr1	154531000	154532537	E071	-16343
chr1	154539789	154539919	E071	-8961
chr1	154539954	154540863	E071	-8017
chr1	154579586	154582633	E071	30706
chr1	154530171	154530966	E072	-17914
chr1	154531000	154532537	E072	-16343
chr1	154539711	154539765	E072	-9115
chr1	154539789	154539919	E072	-8961
chr1	154539954	154540863	E072	-8017
chr1	154579586	154582633	E072	30706
chr1	154530171	154530966	E073	-17914
chr1	154531000	154532537	E073	-16343
chr1	154539711	154539765	E073	-9115
chr1	154539789	154539919	E073	-8961
chr1	154539954	154540863	E073	-8017
chr1	154579586	154582633	E073	30706
chr1	154530171	154530966	E074	-17914
chr1	154531000	154532537	E074	-16343
chr1	154579586	154582633	E074	30706
chr1	154530171	154530966	E081	-17914
chr1	154531000	154532537	E081	-16343
chr1	154539711	154539765	E081	-9115
chr1	154539789	154539919	E081	-8961
chr1	154539954	154540863	E081	-8017
chr1	154579586	154582633	E081	30706
chr1	154530171	154530966	E082	-17914
chr1	154531000	154532537	E082	-16343
chr1	154539711	154539765	E082	-9115
chr1	154539789	154539919	E082	-8961
chr1	154539954	154540863	E082	-8017
chr1	154579586	154582633	E082	30706