rs2273500

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CHRNA4 : Splice Acceptor Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0158 (4751/29922,GnomAD)
C=0149 (4363/29118,TOPMED)
C=0236 (3089/13046,ExAC)
C=0178 (889/5008,1000G)
C=0144 (556/3854,ALSPAC)
C=0141 (522/3708,TWINSUK)

Position: chr20:63355597 (GRCh38.p7) (20q13.33)

Phenotype: ND

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 369 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 20	NC_000020.11:g.63355597T>C
GRCh37.p13 chr 20	NC_000020.10:g.61986949T>C
CHRNA4 RefSeqGene	NG_011931.1:g.10747A>G

Gene: CHRNA4, cholinergic receptor nicotinic alpha 4 subunit(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CHRNA4 transcript variant 1	NM_000744.6:c.	N/A	Intron Variant
CHRNA4 transcript variant 2	NM_001256573.1:c.	N/A	Intron Variant
CHRNA4 transcript variant 3	NR_046317.1:n.	N/A	Intron Variant
CHRNA4 transcript variant X1	XM_011528524.1:c.	N/A	Splice Acceptor Variant
CHRNA4 transcript variant X2	XM_017027624.1:c.	N/A	Intron Variant
CHRNA4 transcript variant X3	XM_017027625.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.846	C=0.154
1000Genomes	American	Sub	694	T=0.890	C=0.110
1000Genomes	East Asian	Sub	1008	T=0.891	C=0.109
1000Genomes	Europe	Sub	1006	T=0.854	C=0.146
1000Genomes	Global	Study-wide	5008	T=0.822	C=0.178
1000Genomes	South Asian	Sub	978	T=0.640	C=0.360
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.856	C=0.144
The Exome Aggregation Consortium	American	Sub	728	T=0.840	C=0.160
The Exome Aggregation Consortium	Asian	Sub	7816	T=0.729	C=0.271
The Exome Aggregation Consortium	Europe	Sub	4356	T=0.808	C=0.192
The Exome Aggregation Consortium	Global	Study-wide	13046	T=0.763	C=0.236
The Exome Aggregation Consortium	Other	Sub	146	T=0.880	C=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.850	C=0.149
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.859	C=0.141

PMID	Title	Author	Journal
26440539	Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence.	Hancock DB	Transl Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs2273500	8E-09	nicotine dependence	26440539

eQTL of rs2273500 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 rs2273500 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 )
chr20	61940682	61941468	E067	-45481
chr20	61952277	61952368	E067	-34581
chr20	61953106	61953152	E067	-33797
chr20	61969576	61969656	E067	-17293
chr20	61983296	61984177	E067	-2772
chr20	61984237	61984327	E067	-2622
chr20	61984510	61984601	E067	-2348
chr20	61984637	61984718	E067	-2231
chr20	61984855	61984906	E067	-2043
chr20	61989177	61989713	E067	2228
chr20	61989714	61989994	E067	2765
chr20	61990171	61990211	E067	3222
chr20	62001862	62003060	E067	14913
chr20	62008420	62008460	E067	21471
chr20	62008583	62009798	E067	21634
chr20	62025289	62026136	E067	38340
chr20	61939928	61939987	E068	-46962
chr20	61940150	61940348	E068	-46601
chr20	61940374	61940428	E068	-46521
chr20	61940484	61940534	E068	-46415
chr20	61940581	61940671	E068	-46278
chr20	61983296	61984177	E068	-2772
chr20	61984237	61984327	E068	-2622
chr20	61984510	61984601	E068	-2348
chr20	61984637	61984718	E068	-2231
chr20	62008583	62009798	E068	21634
chr20	61939767	61939844	E069	-47105
chr20	61939928	61939987	E069	-46962
chr20	61940150	61940348	E069	-46601
chr20	61940374	61940428	E069	-46521
chr20	61940484	61940534	E069	-46415
chr20	61940581	61940671	E069	-46278
chr20	61940682	61941468	E069	-45481
chr20	61976869	61977040	E069	-9909
chr20	61977111	61977181	E069	-9768
chr20	61983296	61984177	E069	-2772
chr20	61984237	61984327	E069	-2622
chr20	61984510	61984601	E069	-2348
chr20	61984637	61984718	E069	-2231
chr20	61989714	61989994	E069	2765
chr20	61990171	61990211	E069	3222
chr20	61990307	61990364	E069	3358
chr20	61991377	61991546	E069	4428
chr20	62001815	62001855	E069	14866
chr20	62008420	62008460	E069	21471
chr20	62009861	62009912	E069	22912
chr20	62010091	62010268	E069	23142
chr20	62010335	62010459	E069	23386
chr20	62013072	62013585	E069	26123
chr20	62025289	62026136	E069	38340
chr20	62026158	62026423	E069	39209
chr20	61976327	61976476	E070	-10473
chr20	61976524	61976762	E070	-10187
chr20	61976869	61977040	E070	-9909
chr20	61983094	61983179	E070	-3770
chr20	61984237	61984327	E070	-2622
chr20	61984510	61984601	E070	-2348
chr20	61984637	61984718	E070	-2231
chr20	61989714	61989994	E070	2765
chr20	62001201	62001489	E070	14252
chr20	62001815	62001855	E070	14866
chr20	62001862	62003060	E070	14913
chr20	62009861	62009912	E070	22912
chr20	62010091	62010268	E070	23142
chr20	62010335	62010459	E070	23386
chr20	62013072	62013585	E070	26123
chr20	62024931	62025253	E070	37982
chr20	62026158	62026423	E070	39209
chr20	62026672	62026738	E070	39723
chr20	62033647	62033822	E070	46698
chr20	62033956	62034031	E070	47007
chr20	62034034	62034084	E070	47085
chr20	62034224	62034385	E070	47275
chr20	62034444	62034523	E070	47495
chr20	62034544	62034598	E070	47595
chr20	62034608	62034695	E070	47659
chr20	62034745	62034795	E070	47796
chr20	62034835	62035037	E070	47886
chr20	61940150	61940348	E071	-46601
chr20	61940374	61940428	E071	-46521
chr20	61940484	61940534	E071	-46415
chr20	61940581	61940671	E071	-46278
chr20	61940682	61941468	E071	-45481
chr20	61943841	61944051	E071	-42898
chr20	61944114	61944308	E071	-42641
chr20	61944447	61944864	E071	-42085
chr20	61983296	61984177	E071	-2772
chr20	61984237	61984327	E071	-2622
chr20	61984510	61984601	E071	-2348
chr20	61984637	61984718	E071	-2231
chr20	61984855	61984906	E071	-2043
chr20	61985031	61985075	E071	-1874
chr20	62008420	62008460	E071	21471
chr20	62008583	62009798	E071	21634
chr20	62009861	62009912	E071	22912
chr20	62010091	62010268	E071	23142
chr20	62013072	62013585	E071	26123
chr20	61939767	61939844	E072	-47105
chr20	61939928	61939987	E072	-46962
chr20	61940150	61940348	E072	-46601
chr20	61940374	61940428	E072	-46521
chr20	61940484	61940534	E072	-46415
chr20	61940581	61940671	E072	-46278
chr20	61940682	61941468	E072	-45481
chr20	61943442	61943614	E072	-43335
chr20	61943841	61944051	E072	-42898
chr20	61944114	61944308	E072	-42641
chr20	61944447	61944864	E072	-42085
chr20	61952162	61952254	E072	-34695
chr20	61952277	61952368	E072	-34581
chr20	61952570	61953054	E072	-33895
chr20	61967787	61967837	E072	-19112
chr20	61967845	61967979	E072	-18970
chr20	61983094	61983179	E072	-3770
chr20	61983296	61984177	E072	-2772
chr20	61984237	61984327	E072	-2622
chr20	61984510	61984601	E072	-2348
chr20	61984637	61984718	E072	-2231
chr20	61989714	61989994	E072	2765
chr20	61990171	61990211	E072	3222
chr20	62001862	62003060	E072	14913
chr20	62008583	62009798	E072	21634
chr20	62009861	62009912	E072	22912
chr20	62010091	62010268	E072	23142
chr20	62010335	62010459	E072	23386
chr20	62013072	62013585	E072	26123
chr20	62024931	62025253	E072	37982
chr20	62025289	62026136	E072	38340
chr20	61940374	61940428	E073	-46521
chr20	61943841	61944051	E073	-42898
chr20	61944114	61944308	E073	-42641
chr20	61944447	61944864	E073	-42085
chr20	61977211	61978004	E073	-8945
chr20	61978047	61978087	E073	-8862
chr20	61978098	61978251	E073	-8698
chr20	61978369	61978409	E073	-8540
chr20	61978511	61978581	E073	-8368
chr20	61983296	61984177	E073	-2772
chr20	61984237	61984327	E073	-2622
chr20	61984510	61984601	E073	-2348
chr20	61984637	61984718	E073	-2231
chr20	61989177	61989713	E073	2228
chr20	61989714	61989994	E073	2765
chr20	61990171	61990211	E073	3222
chr20	61990307	61990364	E073	3358
chr20	61990485	61990630	E073	3536
chr20	61990723	61990816	E073	3774
chr20	61991042	61991248	E073	4093
chr20	61998429	61998695	E073	11480
chr20	62001815	62001855	E073	14866
chr20	62001862	62003060	E073	14913
chr20	62008420	62008460	E073	21471
chr20	62009861	62009912	E073	22912
chr20	62013072	62013585	E073	26123
chr20	62024931	62025253	E073	37982
chr20	62025289	62026136	E073	38340
chr20	62026158	62026423	E073	39209
chr20	61977211	61978004	E074	-8945
chr20	61978047	61978087	E074	-8862
chr20	61978098	61978251	E074	-8698
chr20	61978369	61978409	E074	-8540
chr20	61983296	61984177	E074	-2772
chr20	61984237	61984327	E074	-2622
chr20	61984510	61984601	E074	-2348
chr20	61984637	61984718	E074	-2231
chr20	62008583	62009798	E074	21634
chr20	62009861	62009912	E074	22912
chr20	62010091	62010268	E074	23142
chr20	62010335	62010459	E074	23386
chr20	61940150	61940348	E081	-46601
chr20	61940374	61940428	E081	-46521
chr20	61940484	61940534	E081	-46415
chr20	61940581	61940671	E081	-46278
chr20	61940682	61941468	E081	-45481
chr20	61941477	61941527	E081	-45422
chr20	61943359	61943431	E081	-43518
chr20	61943442	61943614	E081	-43335
chr20	61943841	61944051	E081	-42898
chr20	61944114	61944308	E081	-42641
chr20	61944447	61944864	E081	-42085
chr20	61944990	61945040	E081	-41909
chr20	61945184	61945376	E081	-41573
chr20	61945395	61945435	E081	-41514
chr20	61945438	61945498	E081	-41451
chr20	61946045	61946089	E081	-40860
chr20	61946528	61946652	E081	-40297
chr20	61946693	61946737	E081	-40212
chr20	61946774	61946878	E081	-40071
chr20	61946949	61947029	E081	-39920
chr20	61947199	61947329	E081	-39620
chr20	61947754	61947804	E081	-39145
chr20	61947883	61947949	E081	-39000
chr20	61952570	61953054	E081	-33895
chr20	61953553	61953628	E081	-33321
chr20	61953788	61953838	E081	-33111
chr20	61953862	61953973	E081	-32976
chr20	61954119	61954183	E081	-32766
chr20	61954275	61954349	E081	-32600
chr20	61954350	61954532	E081	-32417
chr20	61956496	61956546	E081	-30403
chr20	61969576	61969656	E081	-17293
chr20	61974055	61974126	E081	-12823
chr20	61974228	61974640	E081	-12309
chr20	61974646	61974813	E081	-12136
chr20	61974841	61974995	E081	-11954
chr20	61975049	61975222	E081	-11727
chr20	61975314	61975430	E081	-11519
chr20	61975498	61975651	E081	-11298
chr20	61975886	61976227	E081	-10722
chr20	61976327	61976476	E081	-10473
chr20	61978098	61978251	E081	-8698
chr20	61978369	61978409	E081	-8540
chr20	61978511	61978581	E081	-8368
chr20	61978686	61978843	E081	-8106
chr20	61978978	61979136	E081	-7813
chr20	61983094	61983179	E081	-3770
chr20	61983296	61984177	E081	-2772
chr20	61984237	61984327	E081	-2622
chr20	61984510	61984601	E081	-2348
chr20	61984637	61984718	E081	-2231
chr20	61984855	61984906	E081	-2043
chr20	61985031	61985075	E081	-1874
chr20	61989121	61989171	E081	2172
chr20	61989714	61989994	E081	2765
chr20	61990171	61990211	E081	3222
chr20	61990307	61990364	E081	3358
chr20	61990485	61990630	E081	3536
chr20	61990723	61990816	E081	3774
chr20	61991042	61991248	E081	4093
chr20	61991377	61991546	E081	4428
chr20	61995364	61995421	E081	8415
chr20	61995465	61995680	E081	8516
chr20	61997104	61997164	E081	10155
chr20	61997308	61997368	E081	10359
chr20	61997670	61998388	E081	10721
chr20	61998429	61998695	E081	11480
chr20	61998905	61999422	E081	11956
chr20	62000404	62000468	E081	13455
chr20	62000560	62000629	E081	13611
chr20	62000788	62000902	E081	13839
chr20	62001201	62001489	E081	14252
chr20	62001815	62001855	E081	14866
chr20	62001862	62003060	E081	14913
chr20	62004055	62004095	E081	17106
chr20	62004232	62004282	E081	17283
chr20	62004467	62004558	E081	17518
chr20	62004713	62005176	E081	17764
chr20	62005357	62005429	E081	18408
chr20	62005443	62005483	E081	18494
chr20	62005518	62005568	E081	18569
chr20	62005585	62005665	E081	18636
chr20	62005724	62005774	E081	18775
chr20	62005816	62006212	E081	18867
chr20	62006455	62006505	E081	19506
chr20	62007509	62007566	E081	20560
chr20	62008420	62008460	E081	21471
chr20	62008583	62009798	E081	21634
chr20	62009861	62009912	E081	22912
chr20	62010091	62010268	E081	23142
chr20	62010335	62010459	E081	23386
chr20	62010489	62010636	E081	23540
chr20	62012618	62013030	E081	25669
chr20	62013072	62013585	E081	26123
chr20	62013630	62013690	E081	26681
chr20	62013693	62013746	E081	26744
chr20	62013801	62013876	E081	26852
chr20	62013895	62013949	E081	26946
chr20	62013993	62014135	E081	27044
chr20	62014732	62015187	E081	27783
chr20	62018419	62018706	E081	31470
chr20	62024140	62024312	E081	37191
chr20	62024389	62024468	E081	37440
chr20	62024503	62024553	E081	37554
chr20	62024931	62025253	E081	37982
chr20	62025289	62026136	E081	38340
chr20	62026158	62026423	E081	39209
chr20	62026672	62026738	E081	39723
chr20	62026836	62026905	E081	39887
chr20	62027002	62027184	E081	40053
chr20	62027294	62027473	E081	40345
chr20	62027509	62027601	E081	40560
chr20	62028032	62028092	E081	41083
chr20	62028118	62028172	E081	41169
chr20	62028210	62028260	E081	41261
chr20	62028378	62028523	E081	41429
chr20	62028524	62028644	E081	41575
chr20	62028812	62028954	E081	41863
chr20	62033647	62033822	E081	46698
chr20	62033956	62034031	E081	47007
chr20	62034034	62034084	E081	47085
chr20	62034224	62034385	E081	47275
chr20	62034444	62034523	E081	47495
chr20	62034544	62034598	E081	47595
chr20	62034608	62034695	E081	47659
chr20	62034745	62034795	E081	47796
chr20	62034835	62035037	E081	47886
chr20	62035118	62035249	E081	48169
chr20	61939928	61939987	E082	-46962
chr20	61944114	61944308	E082	-42641
chr20	61944447	61944864	E082	-42085
chr20	61953788	61953838	E082	-33111
chr20	61953862	61953973	E082	-32976
chr20	61954119	61954183	E082	-32766
chr20	61964787	61964837	E082	-22112
chr20	61964952	61965075	E082	-21874
chr20	61965271	61965325	E082	-21624
chr20	61974055	61974126	E082	-12823
chr20	61974646	61974813	E082	-12136
chr20	61983094	61983179	E082	-3770
chr20	61983296	61984177	E082	-2772
chr20	61984237	61984327	E082	-2622
chr20	61984510	61984601	E082	-2348
chr20	61990485	61990630	E082	3536
chr20	61990723	61990816	E082	3774
chr20	61991042	61991248	E082	4093
chr20	61997104	61997164	E082	10155
chr20	61997308	61997368	E082	10359
chr20	61997670	61998388	E082	10721
chr20	61998429	61998695	E082	11480
chr20	61998905	61999422	E082	11956
chr20	61999423	61999473	E082	12474
chr20	62000560	62000629	E082	13611
chr20	62000788	62000902	E082	13839
chr20	62001201	62001489	E082	14252
chr20	62001815	62001855	E082	14866
chr20	62004055	62004095	E082	17106
chr20	62004232	62004282	E082	17283
chr20	62004467	62004558	E082	17518
chr20	62004713	62005176	E082	17764
chr20	62005357	62005429	E082	18408
chr20	62005443	62005483	E082	18494
chr20	62005518	62005568	E082	18569
chr20	62005585	62005665	E082	18636
chr20	62005724	62005774	E082	18775
chr20	62005816	62006212	E082	18867
chr20	62006455	62006505	E082	19506
chr20	62007509	62007566	E082	20560
chr20	62009861	62009912	E082	22912
chr20	62010091	62010268	E082	23142
chr20	62010335	62010459	E082	23386
chr20	62010489	62010636	E082	23540
chr20	62013072	62013585	E082	26123
chr20	62013630	62013690	E082	26681
chr20	62013693	62013746	E082	26744
chr20	62013801	62013876	E082	26852
chr20	62013895	62013949	E082	26946
chr20	62014732	62015187	E082	27783
chr20	62024931	62025253	E082	37982
chr20	62026672	62026738	E082	39723
chr20	62026836	62026905	E082	39887
chr20	62027002	62027184	E082	40053
chr20	62027294	62027473	E082	40345
chr20	62027509	62027601	E082	40560
chr20	62028032	62028092	E082	41083
chr20	62028118	62028172	E082	41169
chr20	62028210	62028260	E082	41261
chr20	62028378	62028523	E082	41429
chr20	62028524	62028644	E082	41575
chr20	62028812	62028954	E082	41863
chr20	62033647	62033822	E082	46698
chr20	62033956	62034031	E082	47007
chr20	62034034	62034084	E082	47085
chr20	62034224	62034385	E082	47275
chr20	62034444	62034523	E082	47495
chr20	62034544	62034598	E082	47595
chr20	62034608	62034695	E082	47659
chr20	62034745	62034795	E082	47796
chr20	62034835	62035037	E082	47886
chr20	62035118	62035249	E082	48169