rs2390794

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LRRC8C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0303 (9064/29872,GnomAD)
A=0272 (7943/29118,TOPMED)
A=0281 (1408/5008,1000G)
A=0339 (1308/3854,ALSPAC)
A=0335 (1241/3708,TWINSUK)

Position: chr1:89660007 (GRCh38.p7) (1p22.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 233 Enhancers around

Promoter: 33 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.89660007G>A
GRCh37.p13 chr 1	NC_000001.10:g.90125566G>A

Gene: LRRC8C, leucine-rich repeat containing 8 family member C(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LRRC8C transcript	NM_032270.4:c.	N/A	Intron Variant
LRRC8C transcript variant X2	XM_011542282.2:c.	N/A	Intron Variant
LRRC8C transcript variant X3	XM_017002503.1:c.	N/A	Intron Variant
LRRC8C transcript variant X5	XM_017002504.1:c.	N/A	Intron Variant
LRRC8C transcript variant X1	XM_006710960.3:c.	N/A	Genic Upstream Transcript Variant
LRRC8C transcript variant X4	XM_011542283.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.792	A=0.208
1000Genomes	American	Sub	694	G=0.660	A=0.340
1000Genomes	East Asian	Sub	1008	G=0.646	A=0.354
1000Genomes	Europe	Sub	1006	G=0.713	A=0.287
1000Genomes	Global	Study-wide	5008	G=0.719	A=0.281
1000Genomes	South Asian	Sub	978	G=0.740	A=0.260
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.661	A=0.339
The Genome Aggregation Database	African	Sub	8670	G=0.778	A=0.222
The Genome Aggregation Database	American	Sub	834	G=0.600	A=0.400
The Genome Aggregation Database	East Asian	Sub	1606	G=0.624	A=0.376
The Genome Aggregation Database	Europe	Sub	18460	G=0.669	A=0.330
The Genome Aggregation Database	Global	Study-wide	29872	G=0.696	A=0.303
The Genome Aggregation Database	Other	Sub	302	G=0.670	A=0.330
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.727	A=0.272
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.665	A=0.335

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs2390794	0.000123	nicotine smoking	19268276

eQTL of rs2390794 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 rs2390794 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	90081357	90081515	E067	-44051
chr1	90081531	90082042	E067	-43524
chr1	90082510	90082621	E067	-42945
chr1	90082841	90083254	E067	-42312
chr1	90089745	90090242	E067	-35324
chr1	90091986	90092088	E067	-33478
chr1	90092193	90092343	E067	-33223
chr1	90092466	90092682	E067	-32884
chr1	90092883	90093505	E067	-32061
chr1	90093734	90093797	E067	-31769
chr1	90094845	90094935	E067	-30631
chr1	90094991	90095069	E067	-30497
chr1	90095308	90095397	E067	-30169
chr1	90095642	90095682	E067	-29884
chr1	90095762	90095896	E067	-29670
chr1	90096043	90096110	E067	-29456
chr1	90096444	90096544	E067	-29022
chr1	90096957	90097060	E067	-28506
chr1	90097142	90097182	E067	-28384
chr1	90123472	90123854	E067	-1712
chr1	90125004	90125162	E067	-404
chr1	90125294	90125695	E067	0
chr1	90125735	90127057	E067	169
chr1	90127430	90127507	E067	1864
chr1	90133228	90133321	E067	7662
chr1	90133327	90133903	E067	7761
chr1	90167127	90167203	E067	41561
chr1	90167368	90167565	E067	41802
chr1	90167613	90167751	E067	42047
chr1	90174666	90174821	E067	49100
chr1	90174854	90174954	E067	49288
chr1	90081357	90081515	E068	-44051
chr1	90081531	90082042	E068	-43524
chr1	90082510	90082621	E068	-42945
chr1	90082841	90083254	E068	-42312
chr1	90089745	90090242	E068	-35324
chr1	90090528	90090681	E068	-34885
chr1	90090692	90090740	E068	-34826
chr1	90091986	90092088	E068	-33478
chr1	90092193	90092343	E068	-33223
chr1	90092466	90092682	E068	-32884
chr1	90092805	90092878	E068	-32688
chr1	90092883	90093505	E068	-32061
chr1	90094845	90094935	E068	-30631
chr1	90094991	90095069	E068	-30497
chr1	90095308	90095397	E068	-30169
chr1	90095642	90095682	E068	-29884
chr1	90095762	90095896	E068	-29670
chr1	90096043	90096110	E068	-29456
chr1	90096444	90096544	E068	-29022
chr1	90101413	90102245	E068	-23321
chr1	90125004	90125162	E068	-404
chr1	90125294	90125695	E068	0
chr1	90125735	90127057	E068	169
chr1	90135725	90136032	E068	10159
chr1	90137289	90137368	E068	11723
chr1	90164069	90164119	E068	38503
chr1	90164273	90164323	E068	38707
chr1	90164355	90164476	E068	38789
chr1	90164901	90165015	E068	39335
chr1	90167127	90167203	E068	41561
chr1	90167368	90167565	E068	41802
chr1	90167613	90167751	E068	42047
chr1	90174389	90174508	E068	48823
chr1	90174666	90174821	E068	49100
chr1	90174854	90174954	E068	49288
chr1	90081357	90081515	E069	-44051
chr1	90081531	90082042	E069	-43524
chr1	90082510	90082621	E069	-42945
chr1	90082841	90083254	E069	-42312
chr1	90084031	90084091	E069	-41475
chr1	90089745	90090242	E069	-35324
chr1	90090528	90090681	E069	-34885
chr1	90090692	90090740	E069	-34826
chr1	90091986	90092088	E069	-33478
chr1	90092193	90092343	E069	-33223
chr1	90092466	90092682	E069	-32884
chr1	90092805	90092878	E069	-32688
chr1	90092883	90093505	E069	-32061
chr1	90093734	90093797	E069	-31769
chr1	90094845	90094935	E069	-30631
chr1	90094991	90095069	E069	-30497
chr1	90095308	90095397	E069	-30169
chr1	90095642	90095682	E069	-29884
chr1	90095762	90095896	E069	-29670
chr1	90096043	90096110	E069	-29456
chr1	90096444	90096544	E069	-29022
chr1	90096957	90097060	E069	-28506
chr1	90097142	90097182	E069	-28384
chr1	90103203	90103278	E069	-22288
chr1	90121714	90121808	E069	-3758
chr1	90122108	90122188	E069	-3378
chr1	90125294	90125695	E069	0
chr1	90125735	90127057	E069	169
chr1	90156329	90156383	E069	30763
chr1	90167127	90167203	E069	41561
chr1	90167368	90167565	E069	41802
chr1	90167613	90167751	E069	42047
chr1	90174389	90174508	E069	48823
chr1	90174666	90174821	E069	49100
chr1	90174854	90174954	E069	49288
chr1	90081357	90081515	E071	-44051
chr1	90081531	90082042	E071	-43524
chr1	90082510	90082621	E071	-42945
chr1	90082841	90083254	E071	-42312
chr1	90084031	90084091	E071	-41475
chr1	90089745	90090242	E071	-35324
chr1	90090528	90090681	E071	-34885
chr1	90090692	90090740	E071	-34826
chr1	90091986	90092088	E071	-33478
chr1	90092193	90092343	E071	-33223
chr1	90092466	90092682	E071	-32884
chr1	90092805	90092878	E071	-32688
chr1	90092883	90093505	E071	-32061
chr1	90093734	90093797	E071	-31769
chr1	90094845	90094935	E071	-30631
chr1	90094991	90095069	E071	-30497
chr1	90095308	90095397	E071	-30169
chr1	90095642	90095682	E071	-29884
chr1	90095762	90095896	E071	-29670
chr1	90096043	90096110	E071	-29456
chr1	90096444	90096544	E071	-29022
chr1	90101413	90102245	E071	-23321
chr1	90115329	90115530	E071	-10036
chr1	90124777	90124827	E071	-739
chr1	90124878	90124927	E071	-639
chr1	90125004	90125162	E071	-404
chr1	90125294	90125695	E071	0
chr1	90125735	90127057	E071	169
chr1	90127430	90127507	E071	1864
chr1	90133228	90133321	E071	7662
chr1	90133327	90133903	E071	7761
chr1	90157852	90158149	E071	32286
chr1	90158180	90158764	E071	32614
chr1	90160785	90160892	E071	35219
chr1	90161034	90161085	E071	35468
chr1	90161582	90161776	E071	36016
chr1	90161885	90161943	E071	36319
chr1	90162190	90162250	E071	36624
chr1	90167127	90167203	E071	41561
chr1	90167368	90167565	E071	41802
chr1	90167613	90167751	E071	42047
chr1	90174389	90174508	E071	48823
chr1	90081357	90081515	E072	-44051
chr1	90081531	90082042	E072	-43524
chr1	90082510	90082621	E072	-42945
chr1	90082841	90083254	E072	-42312
chr1	90089745	90090242	E072	-35324
chr1	90090528	90090681	E072	-34885
chr1	90090692	90090740	E072	-34826
chr1	90091986	90092088	E072	-33478
chr1	90092193	90092343	E072	-33223
chr1	90092466	90092682	E072	-32884
chr1	90093734	90093797	E072	-31769
chr1	90094845	90094935	E072	-30631
chr1	90094991	90095069	E072	-30497
chr1	90095308	90095397	E072	-30169
chr1	90095642	90095682	E072	-29884
chr1	90095762	90095896	E072	-29670
chr1	90096043	90096110	E072	-29456
chr1	90096444	90096544	E072	-29022
chr1	90096957	90097060	E072	-28506
chr1	90097142	90097182	E072	-28384
chr1	90101413	90102245	E072	-23321
chr1	90123472	90123854	E072	-1712
chr1	90125004	90125162	E072	-404
chr1	90125294	90125695	E072	0
chr1	90125735	90127057	E072	169
chr1	90127430	90127507	E072	1864
chr1	90127811	90127877	E072	2245
chr1	90131609	90131791	E072	6043
chr1	90137289	90137368	E072	11723
chr1	90137739	90138192	E072	12173
chr1	90167127	90167203	E072	41561
chr1	90167368	90167565	E072	41802
chr1	90167613	90167751	E072	42047
chr1	90174389	90174508	E072	48823
chr1	90174666	90174821	E072	49100
chr1	90174854	90174954	E072	49288
chr1	90081357	90081515	E073	-44051
chr1	90081531	90082042	E073	-43524
chr1	90082510	90082621	E073	-42945
chr1	90092883	90093505	E073	-32061
chr1	90094845	90094935	E073	-30631
chr1	90094991	90095069	E073	-30497
chr1	90096444	90096544	E073	-29022
chr1	90096957	90097060	E073	-28506
chr1	90097142	90097182	E073	-28384
chr1	90108858	90108923	E073	-16643
chr1	90125294	90125695	E073	0
chr1	90125735	90127057	E073	169
chr1	90167368	90167565	E073	41802
chr1	90167613	90167751	E073	42047
chr1	90174666	90174821	E073	49100
chr1	90174854	90174954	E073	49288
chr1	90081531	90082042	E074	-43524
chr1	90082510	90082621	E074	-42945
chr1	90082841	90083254	E074	-42312
chr1	90084031	90084091	E074	-41475
chr1	90089745	90090242	E074	-35324
chr1	90090528	90090681	E074	-34885
chr1	90090692	90090740	E074	-34826
chr1	90091986	90092088	E074	-33478
chr1	90092193	90092343	E074	-33223
chr1	90092466	90092682	E074	-32884
chr1	90092805	90092878	E074	-32688
chr1	90092883	90093505	E074	-32061
chr1	90093734	90093797	E074	-31769
chr1	90094845	90094935	E074	-30631
chr1	90094991	90095069	E074	-30497
chr1	90095308	90095397	E074	-30169
chr1	90095642	90095682	E074	-29884
chr1	90095762	90095896	E074	-29670
chr1	90096043	90096110	E074	-29456
chr1	90096444	90096544	E074	-29022
chr1	90096957	90097060	E074	-28506
chr1	90097142	90097182	E074	-28384
chr1	90101413	90102245	E074	-23321
chr1	90122108	90122188	E074	-3378
chr1	90123472	90123854	E074	-1712
chr1	90124067	90124154	E074	-1412
chr1	90124303	90124353	E074	-1213
chr1	90124777	90124827	E074	-739
chr1	90124878	90124927	E074	-639
chr1	90125004	90125162	E074	-404
chr1	90125294	90125695	E074	0
chr1	90125735	90127057	E074	169
chr1	90166417	90166467	E074	40851
chr1	90167127	90167203	E074	41561
chr1	90167368	90167565	E074	41802
chr1	90167613	90167751	E074	42047
chr1	90081357	90081515	E082	-44051
chr1	90081531	90082042	E082	-43524

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	90097428	90100112	E067	-25454
chr1	90100136	90100204	E067	-25362
chr1	90100213	90100322	E067	-25244
chr1	90100375	90100443	E067	-25123
chr1	90097428	90100112	E068	-25454
chr1	90100136	90100204	E068	-25362
chr1	90100213	90100322	E068	-25244
chr1	90100375	90100443	E068	-25123
chr1	90097428	90100112	E069	-25454
chr1	90100136	90100204	E069	-25362
chr1	90100213	90100322	E069	-25244
chr1	90100375	90100443	E069	-25123
chr1	90097428	90100112	E070	-25454
chr1	90097428	90100112	E071	-25454
chr1	90100136	90100204	E071	-25362
chr1	90100213	90100322	E071	-25244
chr1	90100375	90100443	E071	-25123
chr1	90097428	90100112	E072	-25454
chr1	90100136	90100204	E072	-25362
chr1	90100213	90100322	E072	-25244
chr1	90100375	90100443	E072	-25123
chr1	90097428	90100112	E073	-25454
chr1	90100136	90100204	E073	-25362
chr1	90100213	90100322	E073	-25244
chr1	90100375	90100443	E073	-25123
chr1	90097428	90100112	E074	-25454
chr1	90100136	90100204	E074	-25362
chr1	90097428	90100112	E081	-25454
chr1	90100136	90100204	E081	-25362
chr1	90097428	90100112	E082	-25454
chr1	90100136	90100204	E082	-25362
chr1	90100213	90100322	E082	-25244
chr1	90100375	90100443	E082	-25123