rs6428561

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LRRC8C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0435 (13008/29886,GnomAD)
G==0454 (13247/29118,TOPMED)
G==0421 (2109/5008,1000G)
G==0451 (1740/3854,ALSPAC)
G==0454 (1684/3708,TWINSUK)

Position: chr1:89637060 (GRCh38.p7) (1p22.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 277 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.89637060G>A
GRCh37.p13 chr 1	NC_000001.10:g.90102619G>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=0.457	A=0.543
1000Genomes	American	Sub	694	G=0.310	A=0.690
1000Genomes	East Asian	Sub	1008	G=0.231	A=0.769
1000Genomes	Europe	Sub	1006	G=0.495	A=0.505
1000Genomes	Global	Study-wide	5008	G=0.421	A=0.579
1000Genomes	South Asian	Sub	978	G=0.570	A=0.430
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.451	A=0.549
The Genome Aggregation Database	African	Sub	8688	G=0.461	A=0.539
The Genome Aggregation Database	American	Sub	838	G=0.260	A=0.740
The Genome Aggregation Database	East Asian	Sub	1616	G=0.194	A=0.806
The Genome Aggregation Database	Europe	Sub	18444	G=0.450	A=0.549
The Genome Aggregation Database	Global	Study-wide	29886	G=0.435	A=0.564
The Genome Aggregation Database	Other	Sub	300	G=0.540	A=0.460
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.454	A=0.545
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.454	A=0.546

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
rs6428561	0.000134	nicotine smoking	19268276

eQTL of rs6428561 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 rs6428561 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	90053215	90053429	E067	-49190
chr1	90053537	90053636	E067	-48983
chr1	90055187	90055410	E067	-47209
chr1	90055813	90055880	E067	-46739
chr1	90056110	90056322	E067	-46297
chr1	90062458	90062558	E067	-40061
chr1	90063677	90063798	E067	-38821
chr1	90064078	90064360	E067	-38259
chr1	90064402	90064487	E067	-38132
chr1	90064489	90064996	E067	-37623
chr1	90069329	90069707	E067	-32912
chr1	90069864	90069988	E067	-32631
chr1	90081357	90081515	E067	-21104
chr1	90081531	90082042	E067	-20577
chr1	90082510	90082621	E067	-19998
chr1	90082841	90083254	E067	-19365
chr1	90089745	90090242	E067	-12377
chr1	90091986	90092088	E067	-10531
chr1	90092193	90092343	E067	-10276
chr1	90092466	90092682	E067	-9937
chr1	90092883	90093505	E067	-9114
chr1	90093734	90093797	E067	-8822
chr1	90094845	90094935	E067	-7684
chr1	90094991	90095069	E067	-7550
chr1	90095308	90095397	E067	-7222
chr1	90095642	90095682	E067	-6937
chr1	90095762	90095896	E067	-6723
chr1	90096043	90096110	E067	-6509
chr1	90096444	90096544	E067	-6075
chr1	90096957	90097060	E067	-5559
chr1	90097142	90097182	E067	-5437
chr1	90123472	90123854	E067	20853
chr1	90125004	90125162	E067	22385
chr1	90125294	90125695	E067	22675
chr1	90125735	90127057	E067	23116
chr1	90127430	90127507	E067	24811
chr1	90133228	90133321	E067	30609
chr1	90133327	90133903	E067	30708
chr1	90056110	90056322	E068	-46297
chr1	90064078	90064360	E068	-38259
chr1	90064402	90064487	E068	-38132
chr1	90068363	90068732	E068	-33887
chr1	90068761	90068853	E068	-33766
chr1	90068904	90068969	E068	-33650
chr1	90069135	90069289	E068	-33330
chr1	90069329	90069707	E068	-32912
chr1	90069864	90069988	E068	-32631
chr1	90071317	90071647	E068	-30972
chr1	90081357	90081515	E068	-21104
chr1	90081531	90082042	E068	-20577
chr1	90082510	90082621	E068	-19998
chr1	90082841	90083254	E068	-19365
chr1	90089745	90090242	E068	-12377
chr1	90090528	90090681	E068	-11938
chr1	90090692	90090740	E068	-11879
chr1	90091986	90092088	E068	-10531
chr1	90092193	90092343	E068	-10276
chr1	90092466	90092682	E068	-9937
chr1	90092805	90092878	E068	-9741
chr1	90092883	90093505	E068	-9114
chr1	90094845	90094935	E068	-7684
chr1	90094991	90095069	E068	-7550
chr1	90095308	90095397	E068	-7222
chr1	90095642	90095682	E068	-6937
chr1	90095762	90095896	E068	-6723
chr1	90096043	90096110	E068	-6509
chr1	90096444	90096544	E068	-6075
chr1	90101413	90102245	E068	-374
chr1	90125004	90125162	E068	22385
chr1	90125294	90125695	E068	22675
chr1	90125735	90127057	E068	23116
chr1	90135725	90136032	E068	33106
chr1	90137289	90137368	E068	34670
chr1	90053099	90053183	E069	-49436
chr1	90053215	90053429	E069	-49190
chr1	90053537	90053636	E069	-48983
chr1	90055187	90055410	E069	-47209
chr1	90055813	90055880	E069	-46739
chr1	90056110	90056322	E069	-46297
chr1	90062458	90062558	E069	-40061
chr1	90063677	90063798	E069	-38821
chr1	90064078	90064360	E069	-38259
chr1	90064402	90064487	E069	-38132
chr1	90064489	90064996	E069	-37623
chr1	90068761	90068853	E069	-33766
chr1	90068904	90068969	E069	-33650
chr1	90069135	90069289	E069	-33330
chr1	90069329	90069707	E069	-32912
chr1	90069864	90069988	E069	-32631
chr1	90070136	90070242	E069	-32377
chr1	90081357	90081515	E069	-21104
chr1	90081531	90082042	E069	-20577
chr1	90082510	90082621	E069	-19998
chr1	90082841	90083254	E069	-19365
chr1	90084031	90084091	E069	-18528
chr1	90089745	90090242	E069	-12377
chr1	90090528	90090681	E069	-11938
chr1	90090692	90090740	E069	-11879
chr1	90091986	90092088	E069	-10531
chr1	90092193	90092343	E069	-10276
chr1	90092466	90092682	E069	-9937
chr1	90092805	90092878	E069	-9741
chr1	90092883	90093505	E069	-9114
chr1	90093734	90093797	E069	-8822
chr1	90094845	90094935	E069	-7684
chr1	90094991	90095069	E069	-7550
chr1	90095308	90095397	E069	-7222
chr1	90095642	90095682	E069	-6937
chr1	90095762	90095896	E069	-6723
chr1	90096043	90096110	E069	-6509
chr1	90096444	90096544	E069	-6075
chr1	90096957	90097060	E069	-5559
chr1	90097142	90097182	E069	-5437
chr1	90103203	90103278	E069	584
chr1	90121714	90121808	E069	19095
chr1	90122108	90122188	E069	19489
chr1	90125294	90125695	E069	22675
chr1	90125735	90127057	E069	23116
chr1	90056110	90056322	E070	-46297
chr1	90056110	90056322	E071	-46297
chr1	90062458	90062558	E071	-40061
chr1	90064078	90064360	E071	-38259
chr1	90064402	90064487	E071	-38132
chr1	90064489	90064996	E071	-37623
chr1	90069329	90069707	E071	-32912
chr1	90069864	90069988	E071	-32631
chr1	90081357	90081515	E071	-21104
chr1	90081531	90082042	E071	-20577
chr1	90082510	90082621	E071	-19998
chr1	90082841	90083254	E071	-19365
chr1	90084031	90084091	E071	-18528
chr1	90089745	90090242	E071	-12377
chr1	90090528	90090681	E071	-11938
chr1	90090692	90090740	E071	-11879
chr1	90091986	90092088	E071	-10531
chr1	90092193	90092343	E071	-10276
chr1	90092466	90092682	E071	-9937
chr1	90092805	90092878	E071	-9741
chr1	90092883	90093505	E071	-9114
chr1	90093734	90093797	E071	-8822
chr1	90094845	90094935	E071	-7684
chr1	90094991	90095069	E071	-7550
chr1	90095308	90095397	E071	-7222
chr1	90095642	90095682	E071	-6937
chr1	90095762	90095896	E071	-6723
chr1	90096043	90096110	E071	-6509
chr1	90096444	90096544	E071	-6075
chr1	90101413	90102245	E071	-374
chr1	90115329	90115530	E071	12710
chr1	90124777	90124827	E071	22158
chr1	90124878	90124927	E071	22259
chr1	90125004	90125162	E071	22385
chr1	90125294	90125695	E071	22675
chr1	90125735	90127057	E071	23116
chr1	90127430	90127507	E071	24811
chr1	90133228	90133321	E071	30609
chr1	90133327	90133903	E071	30708
chr1	90053215	90053429	E072	-49190
chr1	90053537	90053636	E072	-48983
chr1	90055187	90055410	E072	-47209
chr1	90056110	90056322	E072	-46297
chr1	90059477	90059540	E072	-43079
chr1	90059756	90059953	E072	-42666
chr1	90062458	90062558	E072	-40061
chr1	90064078	90064360	E072	-38259
chr1	90064402	90064487	E072	-38132
chr1	90064489	90064996	E072	-37623
chr1	90068761	90068853	E072	-33766
chr1	90068904	90068969	E072	-33650
chr1	90069135	90069289	E072	-33330
chr1	90069329	90069707	E072	-32912
chr1	90069864	90069988	E072	-32631
chr1	90070779	90070829	E072	-31790
chr1	90071317	90071647	E072	-30972
chr1	90071857	90072041	E072	-30578
chr1	90081357	90081515	E072	-21104
chr1	90081531	90082042	E072	-20577
chr1	90082510	90082621	E072	-19998
chr1	90082841	90083254	E072	-19365
chr1	90089745	90090242	E072	-12377
chr1	90090528	90090681	E072	-11938
chr1	90090692	90090740	E072	-11879
chr1	90091986	90092088	E072	-10531
chr1	90092193	90092343	E072	-10276
chr1	90092466	90092682	E072	-9937
chr1	90093734	90093797	E072	-8822
chr1	90094845	90094935	E072	-7684
chr1	90094991	90095069	E072	-7550
chr1	90095308	90095397	E072	-7222
chr1	90095642	90095682	E072	-6937
chr1	90095762	90095896	E072	-6723
chr1	90096043	90096110	E072	-6509
chr1	90096444	90096544	E072	-6075
chr1	90096957	90097060	E072	-5559
chr1	90097142	90097182	E072	-5437
chr1	90101413	90102245	E072	-374
chr1	90123472	90123854	E072	20853
chr1	90125004	90125162	E072	22385
chr1	90125294	90125695	E072	22675
chr1	90125735	90127057	E072	23116
chr1	90127430	90127507	E072	24811
chr1	90127811	90127877	E072	25192
chr1	90131609	90131791	E072	28990
chr1	90137289	90137368	E072	34670
chr1	90137739	90138192	E072	35120
chr1	90053215	90053429	E073	-49190
chr1	90053537	90053636	E073	-48983
chr1	90056110	90056322	E073	-46297
chr1	90068761	90068853	E073	-33766
chr1	90068904	90068969	E073	-33650
chr1	90069135	90069289	E073	-33330
chr1	90069329	90069707	E073	-32912
chr1	90069864	90069988	E073	-32631
chr1	90070136	90070242	E073	-32377
chr1	90081357	90081515	E073	-21104
chr1	90081531	90082042	E073	-20577
chr1	90082510	90082621	E073	-19998
chr1	90092883	90093505	E073	-9114
chr1	90094845	90094935	E073	-7684
chr1	90094991	90095069	E073	-7550
chr1	90096444	90096544	E073	-6075
chr1	90096957	90097060	E073	-5559
chr1	90097142	90097182	E073	-5437
chr1	90108858	90108923	E073	6239
chr1	90125294	90125695	E073	22675
chr1	90125735	90127057	E073	23116
chr1	90053215	90053429	E074	-49190
chr1	90053537	90053636	E074	-48983
chr1	90055813	90055880	E074	-46739
chr1	90056110	90056322	E074	-46297
chr1	90064078	90064360	E074	-38259
chr1	90064402	90064487	E074	-38132
chr1	90064489	90064996	E074	-37623
chr1	90071317	90071647	E074	-30972
chr1	90071857	90072041	E074	-30578
chr1	90072103	90073481	E074	-29138
chr1	90081531	90082042	E074	-20577
chr1	90082510	90082621	E074	-19998
chr1	90082841	90083254	E074	-19365
chr1	90084031	90084091	E074	-18528
chr1	90089745	90090242	E074	-12377
chr1	90090528	90090681	E074	-11938
chr1	90090692	90090740	E074	-11879
chr1	90091986	90092088	E074	-10531
chr1	90092193	90092343	E074	-10276
chr1	90092466	90092682	E074	-9937
chr1	90092805	90092878	E074	-9741
chr1	90092883	90093505	E074	-9114
chr1	90093734	90093797	E074	-8822
chr1	90094845	90094935	E074	-7684
chr1	90094991	90095069	E074	-7550
chr1	90095308	90095397	E074	-7222
chr1	90095642	90095682	E074	-6937
chr1	90095762	90095896	E074	-6723
chr1	90096043	90096110	E074	-6509
chr1	90096444	90096544	E074	-6075
chr1	90096957	90097060	E074	-5559
chr1	90097142	90097182	E074	-5437
chr1	90101413	90102245	E074	-374
chr1	90122108	90122188	E074	19489
chr1	90123472	90123854	E074	20853
chr1	90124067	90124154	E074	21448
chr1	90124303	90124353	E074	21684
chr1	90124777	90124827	E074	22158
chr1	90124878	90124927	E074	22259
chr1	90125004	90125162	E074	22385
chr1	90125294	90125695	E074	22675
chr1	90125735	90127057	E074	23116
chr1	90065695	90065791	E081	-36828
chr1	90065912	90065962	E081	-36657
chr1	90066124	90066292	E081	-36327
chr1	90066419	90066551	E081	-36068
chr1	90066585	90066635	E081	-35984
chr1	90056110	90056322	E082	-46297
chr1	90062458	90062558	E082	-40061
chr1	90081357	90081515	E082	-21104
chr1	90081531	90082042	E082	-20577

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	90097428	90100112	E067	-2507
chr1	90100136	90100204	E067	-2415
chr1	90100213	90100322	E067	-2297
chr1	90100375	90100443	E067	-2176
chr1	90097428	90100112	E068	-2507
chr1	90100136	90100204	E068	-2415
chr1	90100213	90100322	E068	-2297
chr1	90100375	90100443	E068	-2176
chr1	90097428	90100112	E069	-2507
chr1	90100136	90100204	E069	-2415
chr1	90100213	90100322	E069	-2297
chr1	90100375	90100443	E069	-2176
chr1	90097428	90100112	E070	-2507
chr1	90097428	90100112	E071	-2507
chr1	90100136	90100204	E071	-2415
chr1	90100213	90100322	E071	-2297
chr1	90100375	90100443	E071	-2176
chr1	90097428	90100112	E072	-2507
chr1	90100136	90100204	E072	-2415
chr1	90100213	90100322	E072	-2297
chr1	90100375	90100443	E072	-2176
chr1	90097428	90100112	E073	-2507
chr1	90100136	90100204	E073	-2415
chr1	90100213	90100322	E073	-2297
chr1	90100375	90100443	E073	-2176
chr1	90097428	90100112	E074	-2507
chr1	90100136	90100204	E074	-2415
chr1	90097428	90100112	E081	-2507
chr1	90100136	90100204	E081	-2415
chr1	90097428	90100112	E082	-2507
chr1	90100136	90100204	E082	-2415
chr1	90100213	90100322	E082	-2297
chr1	90100375	90100443	E082	-2176