rs2645339

Homo sapiens
G>A
GRM6 : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
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)
chr5:178989062 (GRCh38.p7) (5q35.3)
ND
GWASdb2
4   publication(s)
See rs on genome
3 Enhancers around
74 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.178989062G>A
GRCh37.p13 chr 5NC_000005.9:g.178416063G>A
GRM6 RefSeqGeneNG_008105.1:g.11062C>T

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

Molecule type Change Amino acid[Codon] SO Term
GRM6 transcriptNM_000843.3:c.122...NM_000843.3:c.1227C>TY [TAC]> Y [TAT]Coding Sequence Variant
metabotropic glutamate receptor 6 precursorNP_000834.2:p.Tyr...NP_000834.2:p.Tyr409=Y [Tyr]> Y [Tyr]Synonymous Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.434A=0.566
The Exome Aggregation ConsortiumAmericanSub21632G=0.511A=0.488
The Exome Aggregation ConsortiumAsianSub24932G=0.500A=0.499
The Exome Aggregation ConsortiumEuropeSub72256G=0.453A=0.546
The Exome Aggregation ConsortiumGlobalStudy-wide119704G=0.474A=0.525
The Exome Aggregation ConsortiumOtherSub884G=0.510A=0.490
The Genome Aggregation DatabaseAfricanSub8670G=0.611A=0.389
The Genome Aggregation DatabaseAmericanSub836G=0.450A=0.550
The Genome Aggregation DatabaseEast AsianSub1612G=0.436A=0.564
The Genome Aggregation DatabaseEuropeSub18402G=0.439A=0.560
The Genome Aggregation DatabaseGlobalStudy-wide29820G=0.490A=0.509
The Genome Aggregation DatabaseOtherSub300G=0.480A=0.520
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.539A=0.460
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.442A=0.558
PMID Title Author Journal
27034204Association of ZNF644, GRM6, and CTNND2 genes with high myopia in the Han Chinese population: Jiangsu Eye Study.Wang HEye (Lond)
18227835Alpha-5/alpha-3 nicotinic receptor subunit alleles increase risk for heavy smoking.Berrettini WMol Psychiatry
19862333Sequence variations of GRM6 in patients with high myopia.Xu XMol Vis
22719919Glutamate and synaptic plasticity systems and smoking behavior: results from a genetic association study.dos Santos VAPLoS One

P-Value

SNP ID p-value Traits Study
rs26453390.000272nicotine dependence18227835

eQTL of rs2645339 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 rs2645339 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 )
chr5178452086178452157E07036023
chr5178421049178421132E0814986
chr5178452086178452157E08236023



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr5178367155178367205E067-48858
chr5178367410178367578E067-48485
chr5178367604178368729E067-47334
chr5178368748178368865E067-47198
chr5178450263178450345E06734200
chr5178450387178451325E06734324
chr5178451357178451465E06735294
chr5178367410178367578E068-48485
chr5178367604178368729E068-47334
chr5178368748178368865E068-47198
chr5178450263178450345E06834200
chr5178450387178451325E06834324
chr5178451357178451465E06835294
chr5178367155178367205E069-48858
chr5178367410178367578E069-48485
chr5178367604178368729E069-47334
chr5178368748178368865E069-47198
chr5178450263178450345E06934200
chr5178450387178451325E06934324
chr5178451357178451465E06935294
chr5178367155178367205E070-48858
chr5178367410178367578E070-48485
chr5178367604178368729E070-47334
chr5178368748178368865E070-47198
chr5178421423178421473E0705360
chr5178421625178421933E0705562
chr5178422051178422101E0705988
chr5178450263178450345E07034200
chr5178450387178451325E07034324
chr5178451357178451465E07035294
chr5178367410178367578E071-48485
chr5178367604178368729E071-47334
chr5178368748178368865E071-47198
chr5178450263178450345E07134200
chr5178450387178451325E07134324
chr5178451357178451465E07135294
chr5178367155178367205E072-48858
chr5178367410178367578E072-48485
chr5178367604178368729E072-47334
chr5178368748178368865E072-47198
chr5178450263178450345E07234200
chr5178450387178451325E07234324
chr5178451357178451465E07235294
chr5178367155178367205E073-48858
chr5178367410178367578E073-48485
chr5178367604178368729E073-47334
chr5178368748178368865E073-47198
chr5178450263178450345E07334200
chr5178450387178451325E07334324
chr5178451357178451465E07335294
chr5178367410178367578E074-48485
chr5178367604178368729E074-47334
chr5178368748178368865E074-47198
chr5178450263178450345E07434200
chr5178450387178451325E07434324
chr5178451357178451465E07435294
chr5178367155178367205E081-48858
chr5178367410178367578E081-48485
chr5178367604178368729E081-47334
chr5178368748178368865E081-47198
chr5178450263178450345E08134200
chr5178450387178451325E08134324
chr5178451357178451465E08135294
chr5178367155178367205E082-48858
chr5178367410178367578E082-48485
chr5178367604178368729E082-47334
chr5178368748178368865E082-47198
chr5178421423178421473E0825360
chr5178421625178421933E0825562
chr5178422051178422101E0825988
chr5178422202178422393E0826139
chr5178450263178450345E08234200
chr5178450387178451325E08234324
chr5178451357178451465E08235294