rs2238043

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CACNA1C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0492 (14718/29914,GnomAD)
A=0489 (14239/29118,TOPMED)
G==0469 (2350/5008,1000G)
A=0430 (1659/3854,ALSPAC)
A=0426 (1579/3708,TWINSUK)

Position: chr12:2166497 (GRCh38.p7) (12p13.33)

Phenotype: ND

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 230 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.2166497G>A
GRCh37.p13 chr 12	NC_000012.11:g.2275663G>A
CACNA1C RefSeqGene	LRG_334

Gene: CACNA1C, calcium voltage-gated channel subunit alpha1 C(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACNA1C transcript variant 18	NM_000719.6:c.	N/A	Intron Variant
CACNA1C transcript variant 2	NM_001129827.1:c.	N/A	Intron Variant
CACNA1C transcript variant 3	NM_001129829.1:c.	N/A	Intron Variant
CACNA1C transcript variant 4	NM_001129830.2:c.	N/A	Intron Variant
CACNA1C transcript variant 5	NM_001129831.1:c.	N/A	Intron Variant
CACNA1C transcript variant 6	NM_001129832.1:c.	N/A	Intron Variant
CACNA1C transcript variant 7	NM_001129833.1:c.	N/A	Intron Variant
CACNA1C transcript variant 8	NM_001129834.1:c.	N/A	Intron Variant
CACNA1C transcript variant 9	NM_001129835.1:c.	N/A	Intron Variant
CACNA1C transcript variant 10	NM_001129836.1:c.	N/A	Intron Variant
CACNA1C transcript variant 11	NM_001129837.1:c.	N/A	Intron Variant
CACNA1C transcript variant 12	NM_001129838.1:c.	N/A	Intron Variant
CACNA1C transcript variant 13	NM_001129839.1:c.	N/A	Intron Variant
CACNA1C transcript variant 14	NM_001129840.1:c.	N/A	Intron Variant
CACNA1C transcript variant 15	NM_001129841.1:c.	N/A	Intron Variant
CACNA1C transcript variant 16	NM_001129842.1:c.	N/A	Intron Variant
CACNA1C transcript variant 17	NM_001129843.1:c.	N/A	Intron Variant
CACNA1C transcript variant 19	NM_001129844.1:c.	N/A	Intron Variant
CACNA1C transcript variant 20	NM_001129846.1:c.	N/A	Intron Variant
CACNA1C transcript variant 21	NM_001167623.1:c.	N/A	Intron Variant
CACNA1C transcript variant 22	NM_001167624.2:c.	N/A	Intron Variant
CACNA1C transcript variant 23	NM_001167625.1:c.	N/A	Intron Variant
CACNA1C transcript variant 1	NM_199460.3:c.	N/A	Intron Variant
CACNA1C transcript variant X30	XM_006719017.2:c.	N/A	Intron Variant
CACNA1C transcript variant X28	XM_011521020.2:c.	N/A	Intron Variant
CACNA1C transcript variant X33	XM_011521023.2:c.	N/A	Intron Variant
CACNA1C transcript variant X1	XM_017019926.1:c.	N/A	Intron Variant
CACNA1C transcript variant X2	XM_017019927.1:c.	N/A	Intron Variant
CACNA1C transcript variant X3	XM_017019928.1:c.	N/A	Intron Variant
CACNA1C transcript variant X4	XM_017019929.1:c.	N/A	Intron Variant
CACNA1C transcript variant X5	XM_017019930.1:c.	N/A	Intron Variant
CACNA1C transcript variant X6	XM_017019931.1:c.	N/A	Intron Variant
CACNA1C transcript variant X7	XM_017019932.1:c.	N/A	Intron Variant
CACNA1C transcript variant X8	XM_017019933.1:c.	N/A	Intron Variant
CACNA1C transcript variant X9	XM_017019934.1:c.	N/A	Intron Variant
CACNA1C transcript variant X10	XM_017019935.1:c.	N/A	Intron Variant
CACNA1C transcript variant X11	XM_017019936.1:c.	N/A	Intron Variant
CACNA1C transcript variant X12	XM_017019937.1:c.	N/A	Intron Variant
CACNA1C transcript variant X13	XM_017019938.1:c.	N/A	Intron Variant
CACNA1C transcript variant X14	XM_017019939.1:c.	N/A	Intron Variant
CACNA1C transcript variant X15	XM_017019940.1:c.	N/A	Intron Variant
CACNA1C transcript variant X16	XM_017019941.1:c.	N/A	Intron Variant
CACNA1C transcript variant X17	XM_017019942.1:c.	N/A	Intron Variant
CACNA1C transcript variant X18	XM_017019943.1:c.	N/A	Intron Variant
CACNA1C transcript variant X19	XM_017019944.1:c.	N/A	Intron Variant
CACNA1C transcript variant X20	XM_017019945.1:c.	N/A	Intron Variant
CACNA1C transcript variant X21	XM_017019946.1:c.	N/A	Intron Variant
CACNA1C transcript variant X22	XM_017019947.1:c.	N/A	Intron Variant
CACNA1C transcript variant X23	XM_017019948.1:c.	N/A	Intron Variant
CACNA1C transcript variant X24	XM_017019949.1:c.	N/A	Intron Variant
CACNA1C transcript variant X25	XM_017019950.1:c.	N/A	Intron Variant
CACNA1C transcript variant X26	XM_017019951.1:c.	N/A	Intron Variant
CACNA1C transcript variant X27	XM_017019952.1:c.	N/A	Intron Variant
CACNA1C transcript variant X29	XM_017019953.1:c.	N/A	Intron Variant
CACNA1C transcript variant X31	XM_017019954.1:c.	N/A	Intron Variant
CACNA1C transcript variant X32	XM_017019955.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.430	A=0.570
1000Genomes	American	Sub	694	G=0.570	A=0.430
1000Genomes	East Asian	Sub	1008	G=0.405	A=0.595
1000Genomes	Europe	Sub	1006	G=0.575	A=0.425
1000Genomes	Global	Study-wide	5008	G=0.469	A=0.531
1000Genomes	South Asian	Sub	978	G=0.410	A=0.590
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.570	A=0.430
The Genome Aggregation Database	African	Sub	8708	G=0.446	A=0.554
The Genome Aggregation Database	American	Sub	836	G=0.580	A=0.420
The Genome Aggregation Database	East Asian	Sub	1618	G=0.410	A=0.590
The Genome Aggregation Database	Europe	Sub	18452	G=0.541	A=0.458
The Genome Aggregation Database	Global	Study-wide	29914	G=0.508	A=0.492
The Genome Aggregation Database	Other	Sub	300	G=0.590	A=0.410
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.511	A=0.489
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.574	A=0.426

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet
20723887	Mood disorder susceptibility gene CACNA1C modifies mood-related behaviors in mice and interacts with sex to influence behavior in mice and diagnosis in humans.	Dao DT	Biol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs2238043	0.000397	nicotine smoking	19268276

eQTL of rs2238043 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 rs2238043 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 )
chr12	2235868	2235953	E067	-39710
chr12	2260656	2260840	E067	-14823
chr12	2260844	2261018	E067	-14645
chr12	2261063	2261221	E067	-14442
chr12	2261256	2261355	E067	-14308
chr12	2263038	2263102	E067	-12561
chr12	2263184	2263636	E067	-12027
chr12	2263721	2263799	E067	-11864
chr12	2263883	2264024	E067	-11639
chr12	2264048	2264169	E067	-11494
chr12	2264316	2264366	E067	-11297
chr12	2264651	2264803	E067	-10860
chr12	2270666	2271263	E067	-4400
chr12	2271273	2271389	E067	-4274
chr12	2288668	2288881	E067	13005
chr12	2292867	2292978	E067	17204
chr12	2293012	2293746	E067	17349
chr12	2314419	2314502	E067	38756
chr12	2322150	2323204	E067	46487
chr12	2323262	2323317	E067	47599
chr12	2323376	2323444	E067	47713
chr12	2323524	2323570	E067	47861
chr12	2323579	2323833	E067	47916
chr12	2263038	2263102	E068	-12561
chr12	2263184	2263636	E068	-12027
chr12	2263721	2263799	E068	-11864
chr12	2263883	2264024	E068	-11639
chr12	2264048	2264169	E068	-11494
chr12	2264316	2264366	E068	-11297
chr12	2264651	2264803	E068	-10860
chr12	2270236	2270300	E068	-5363
chr12	2270418	2270522	E068	-5141
chr12	2270527	2270650	E068	-5013
chr12	2270666	2271263	E068	-4400
chr12	2305071	2305157	E068	29408
chr12	2305315	2305365	E068	29652
chr12	2305650	2305916	E068	29987
chr12	2305927	2306092	E068	30264
chr12	2306318	2306427	E068	30655
chr12	2307168	2307962	E068	31505
chr12	2321898	2321988	E068	46235
chr12	2321999	2322089	E068	46336
chr12	2322150	2323204	E068	46487
chr12	2323524	2323570	E068	47861
chr12	2323579	2323833	E068	47916
chr12	2323953	2324046	E068	48290
chr12	2259932	2260333	E069	-15330
chr12	2260656	2260840	E069	-14823
chr12	2260844	2261018	E069	-14645
chr12	2261063	2261221	E069	-14442
chr12	2270527	2270650	E069	-5013
chr12	2270666	2271263	E069	-4400
chr12	2271273	2271389	E069	-4274
chr12	2271440	2271512	E069	-4151
chr12	2271550	2271659	E069	-4004
chr12	2272262	2273519	E069	-2144
chr12	2288668	2288881	E069	13005
chr12	2288950	2289055	E069	13287
chr12	2289120	2290123	E069	13457
chr12	2293012	2293746	E069	17349
chr12	2322150	2323204	E069	46487
chr12	2323262	2323317	E069	47599
chr12	2323376	2323444	E069	47713
chr12	2323524	2323570	E069	47861
chr12	2323579	2323833	E069	47916
chr12	2293012	2293746	E070	17349
chr12	2301267	2301437	E070	25604
chr12	2301482	2301560	E070	25819
chr12	2301592	2301687	E070	25929
chr12	2322150	2323204	E070	46487
chr12	2323262	2323317	E070	47599
chr12	2323376	2323444	E070	47713
chr12	2259932	2260333	E071	-15330
chr12	2260656	2260840	E071	-14823
chr12	2260844	2261018	E071	-14645
chr12	2261063	2261221	E071	-14442
chr12	2270527	2270650	E071	-5013
chr12	2270666	2271263	E071	-4400
chr12	2271273	2271389	E071	-4274
chr12	2271440	2271512	E071	-4151
chr12	2271550	2271659	E071	-4004
chr12	2272262	2273519	E071	-2144
chr12	2288668	2288881	E071	13005
chr12	2288950	2289055	E071	13287
chr12	2289120	2290123	E071	13457
chr12	2321898	2321988	E071	46235
chr12	2321999	2322089	E071	46336
chr12	2322150	2323204	E071	46487
chr12	2323262	2323317	E071	47599
chr12	2323376	2323444	E071	47713
chr12	2323524	2323570	E071	47861
chr12	2323579	2323833	E071	47916
chr12	2323953	2324046	E071	48290
chr12	2234129	2234402	E072	-41261
chr12	2250120	2250228	E072	-25435
chr12	2250564	2250645	E072	-25018
chr12	2250663	2250743	E072	-24920
chr12	2250774	2250947	E072	-24716
chr12	2250954	2251024	E072	-24639
chr12	2251355	2251562	E072	-24101
chr12	2259932	2260333	E072	-15330
chr12	2260656	2260840	E072	-14823
chr12	2260844	2261018	E072	-14645
chr12	2261063	2261221	E072	-14442
chr12	2261256	2261355	E072	-14308
chr12	2261403	2261488	E072	-14175
chr12	2261525	2261719	E072	-13944
chr12	2264316	2264366	E072	-11297
chr12	2264651	2264803	E072	-10860
chr12	2270418	2270522	E072	-5141
chr12	2270527	2270650	E072	-5013
chr12	2270666	2271263	E072	-4400
chr12	2271273	2271389	E072	-4274
chr12	2288668	2288881	E072	13005
chr12	2288950	2289055	E072	13287
chr12	2289120	2290123	E072	13457
chr12	2303246	2303395	E072	27583
chr12	2317469	2317561	E072	41806
chr12	2317584	2317634	E072	41921
chr12	2322150	2323204	E072	46487
chr12	2323262	2323317	E072	47599
chr12	2323376	2323444	E072	47713
chr12	2323524	2323570	E072	47861
chr12	2323579	2323833	E072	47916
chr12	2234129	2234402	E073	-41261
chr12	2246264	2246314	E073	-29349
chr12	2259932	2260333	E073	-15330
chr12	2263038	2263102	E073	-12561
chr12	2263184	2263636	E073	-12027
chr12	2263721	2263799	E073	-11864
chr12	2263883	2264024	E073	-11639
chr12	2264048	2264169	E073	-11494
chr12	2264316	2264366	E073	-11297
chr12	2264651	2264803	E073	-10860
chr12	2270418	2270522	E073	-5141
chr12	2270527	2270650	E073	-5013
chr12	2270666	2271263	E073	-4400
chr12	2271273	2271389	E073	-4274
chr12	2271440	2271512	E073	-4151
chr12	2271550	2271659	E073	-4004
chr12	2278442	2278609	E073	2779
chr12	2278680	2278960	E073	3017
chr12	2278971	2279031	E073	3308
chr12	2279225	2279433	E073	3562
chr12	2279598	2279867	E073	3935
chr12	2279882	2280142	E073	4219
chr12	2280191	2280264	E073	4528
chr12	2280377	2280510	E073	4714
chr12	2280548	2280716	E073	4885
chr12	2280743	2281021	E073	5080
chr12	2281071	2281612	E073	5408
chr12	2288385	2288452	E073	12722
chr12	2288668	2288881	E073	13005
chr12	2288950	2289055	E073	13287
chr12	2289120	2290123	E073	13457
chr12	2293012	2293746	E073	17349
chr12	2316985	2317025	E073	41322
chr12	2317330	2317380	E073	41667
chr12	2317469	2317561	E073	41806
chr12	2317584	2317634	E073	41921
chr12	2321898	2321988	E073	46235
chr12	2321999	2322089	E073	46336
chr12	2322150	2323204	E073	46487
chr12	2323262	2323317	E073	47599
chr12	2323376	2323444	E073	47713
chr12	2323524	2323570	E073	47861
chr12	2323579	2323833	E073	47916
chr12	2323953	2324046	E073	48290
chr12	2324076	2324149	E073	48413
chr12	2324215	2324289	E073	48552
chr12	2324450	2324593	E073	48787
chr12	2324808	2324922	E073	49145
chr12	2325020	2325159	E073	49357
chr12	2250120	2250228	E074	-25435
chr12	2259932	2260333	E074	-15330
chr12	2260656	2260840	E074	-14823
chr12	2260844	2261018	E074	-14645
chr12	2261063	2261221	E074	-14442
chr12	2271273	2271389	E074	-4274
chr12	2271440	2271512	E074	-4151
chr12	2271550	2271659	E074	-4004
chr12	2271692	2271742	E074	-3921
chr12	2271858	2271918	E074	-3745
chr12	2272051	2272168	E074	-3495
chr12	2272262	2273519	E074	-2144
chr12	2273710	2273760	E074	-1903
chr12	2273773	2273911	E074	-1752
chr12	2273996	2274175	E074	-1488
chr12	2293012	2293746	E074	17349
chr12	2293817	2293913	E074	18154
chr12	2229889	2229973	E081	-45690
chr12	2235868	2235953	E081	-39710
chr12	2259932	2260333	E081	-15330
chr12	2260656	2260840	E081	-14823
chr12	2300728	2300930	E081	25065
chr12	2301267	2301437	E081	25604
chr12	2301482	2301560	E081	25819
chr12	2301592	2301687	E081	25929
chr12	2301879	2301952	E081	26216
chr12	2301958	2302045	E081	26295
chr12	2316985	2317025	E081	41322
chr12	2317330	2317380	E081	41667
chr12	2317469	2317561	E081	41806
chr12	2317584	2317634	E081	41921
chr12	2318453	2318723	E081	42790
chr12	2318806	2319237	E081	43143
chr12	2319486	2319582	E081	43823
chr12	2319741	2319797	E081	44078
chr12	2320488	2320751	E081	44825
chr12	2320758	2320836	E081	45095
chr12	2321276	2321326	E081	45613
chr12	2321898	2321988	E081	46235
chr12	2321999	2322089	E081	46336
chr12	2322150	2323204	E081	46487
chr12	2323262	2323317	E081	47599
chr12	2323376	2323444	E081	47713
chr12	2323524	2323570	E081	47861
chr12	2323579	2323833	E081	47916
chr12	2323953	2324046	E081	48290
chr12	2324076	2324149	E081	48413
chr12	2255065	2255115	E082	-20548
chr12	2282069	2282259	E082	6406
chr12	2307168	2307962	E082	31505
chr12	2320488	2320751	E082	44825
chr12	2320758	2320836	E082	45095
chr12	2321898	2321988	E082	46235
chr12	2321999	2322089	E082	46336
chr12	2322150	2323204	E082	46487
chr12	2323262	2323317	E082	47599
chr12	2323376	2323444	E082	47713