rs2645339

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

GRM6 : Synonymous Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0474 (56783/119704,ExAC)
G==0490 (14621/29820,GnomAD)
A=0460 (13417/29118,TOPMED)
G==0488 (6350/13006,GO-ESP)
G==0434 (1672/3854,ALSPAC)
G==0442 (1640/3708,TWINSUK)

Position: chr5:178989062 (GRCh38.p7) (5q35.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 3 Enhancers around

Promoter: 74 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.178989062G>A
GRCh37.p13 chr 5	NC_000005.9:g.178416063G>A
GRM6 RefSeqGene	NG_008105.1:g.11062C>T

Gene: GRM6, glutamate metabotropic receptor 6(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GRM6 transcript	NM_000843.3:c.122...NM_000843.3:c.1227C>T	Y [TAC]> Y [TAT]	Coding Sequence Variant
metabotropic glutamate receptor 6 precursor	NP_000834.2:p.Tyr...NP_000834.2:p.Tyr409=	Y [Tyr]> Y [Tyr]	Synonymous Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.434	A=0.566
The Exome Aggregation Consortium	American	Sub	21632	G=0.511	A=0.488
The Exome Aggregation Consortium	Asian	Sub	24932	G=0.500	A=0.499
The Exome Aggregation Consortium	Europe	Sub	72256	G=0.453	A=0.546
The Exome Aggregation Consortium	Global	Study-wide	119704	G=0.474	A=0.525
The Exome Aggregation Consortium	Other	Sub	884	G=0.510	A=0.490
The Genome Aggregation Database	African	Sub	8670	G=0.611	A=0.389
The Genome Aggregation Database	American	Sub	836	G=0.450	A=0.550
The Genome Aggregation Database	East Asian	Sub	1612	G=0.436	A=0.564
The Genome Aggregation Database	Europe	Sub	18402	G=0.439	A=0.560
The Genome Aggregation Database	Global	Study-wide	29820	G=0.490	A=0.509
The Genome Aggregation Database	Other	Sub	300	G=0.480	A=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.539	A=0.460
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.442	A=0.558

PMID	Title	Author	Journal
27034204	Association of ZNF644, GRM6, and CTNND2 genes with high myopia in the Han Chinese population: Jiangsu Eye Study.	Wang H	Eye (Lond)
18227835	Alpha-5/alpha-3 nicotinic receptor subunit alleles increase risk for heavy smoking.	Berrettini W	Mol Psychiatry
19862333	Sequence variations of GRM6 in patients with high myopia.	Xu X	Mol Vis
22719919	Glutamate and synaptic plasticity systems and smoking behavior: results from a genetic association study.	dos Santos VA	PLoS One

SNP ID	p-value	Traits	Study
rs2645339	0.000272	nicotine dependence	18227835

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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 )
chr5	178452086	178452157	E070	36023
chr5	178421049	178421132	E081	4986
chr5	178452086	178452157	E082	36023

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	178367155	178367205	E067	-48858
chr5	178367410	178367578	E067	-48485
chr5	178367604	178368729	E067	-47334
chr5	178368748	178368865	E067	-47198
chr5	178450263	178450345	E067	34200
chr5	178450387	178451325	E067	34324
chr5	178451357	178451465	E067	35294
chr5	178367410	178367578	E068	-48485
chr5	178367604	178368729	E068	-47334
chr5	178368748	178368865	E068	-47198
chr5	178450263	178450345	E068	34200
chr5	178450387	178451325	E068	34324
chr5	178451357	178451465	E068	35294
chr5	178367155	178367205	E069	-48858
chr5	178367410	178367578	E069	-48485
chr5	178367604	178368729	E069	-47334
chr5	178368748	178368865	E069	-47198
chr5	178450263	178450345	E069	34200
chr5	178450387	178451325	E069	34324
chr5	178451357	178451465	E069	35294
chr5	178367155	178367205	E070	-48858
chr5	178367410	178367578	E070	-48485
chr5	178367604	178368729	E070	-47334
chr5	178368748	178368865	E070	-47198
chr5	178421423	178421473	E070	5360
chr5	178421625	178421933	E070	5562
chr5	178422051	178422101	E070	5988
chr5	178450263	178450345	E070	34200
chr5	178450387	178451325	E070	34324
chr5	178451357	178451465	E070	35294
chr5	178367410	178367578	E071	-48485
chr5	178367604	178368729	E071	-47334
chr5	178368748	178368865	E071	-47198
chr5	178450263	178450345	E071	34200
chr5	178450387	178451325	E071	34324
chr5	178451357	178451465	E071	35294
chr5	178367155	178367205	E072	-48858
chr5	178367410	178367578	E072	-48485
chr5	178367604	178368729	E072	-47334
chr5	178368748	178368865	E072	-47198
chr5	178450263	178450345	E072	34200
chr5	178450387	178451325	E072	34324
chr5	178451357	178451465	E072	35294
chr5	178367155	178367205	E073	-48858
chr5	178367410	178367578	E073	-48485
chr5	178367604	178368729	E073	-47334
chr5	178368748	178368865	E073	-47198
chr5	178450263	178450345	E073	34200
chr5	178450387	178451325	E073	34324
chr5	178451357	178451465	E073	35294
chr5	178367410	178367578	E074	-48485
chr5	178367604	178368729	E074	-47334
chr5	178368748	178368865	E074	-47198
chr5	178450263	178450345	E074	34200
chr5	178450387	178451325	E074	34324
chr5	178451357	178451465	E074	35294
chr5	178367155	178367205	E081	-48858
chr5	178367410	178367578	E081	-48485
chr5	178367604	178368729	E081	-47334
chr5	178368748	178368865	E081	-47198
chr5	178450263	178450345	E081	34200
chr5	178450387	178451325	E081	34324
chr5	178451357	178451465	E081	35294
chr5	178367155	178367205	E082	-48858
chr5	178367410	178367578	E082	-48485
chr5	178367604	178368729	E082	-47334
chr5	178368748	178368865	E082	-47198
chr5	178421423	178421473	E082	5360
chr5	178421625	178421933	E082	5562
chr5	178422051	178422101	E082	5988
chr5	178422202	178422393	E082	6139
chr5	178450263	178450345	E082	34200
chr5	178450387	178451325	E082	34324
chr5	178451357	178451465	E082	35294

rs2645339

Genomic Coordinates

Gene: GRM6, glutamate metabotropic receptor 6(minus strand)

Population Frequency

P-Value

eQTL of rs2645339 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2645339 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)