rs2546657

Homo sapiens
T>A
TRPC7 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0346 (10373/29932,GnomAD)
T==0312 (9112/29118,TOPMED)
T==0337 (1688/5008,1000G)
T==0367 (1415/3854,ALSPAC)
T==0361 (1337/3708,TWINSUK)
chr5:136348047 (GRCh38.p7) (5q31.1)
ND
GWASdb2
1   publication(s)
See rs on genome
1 Enhancer around
3 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.136348047T>A
GRCh37.p13 chr 5NC_000005.9:g.135683735T>A

Gene: TRPC7, transient receptor potential cation channel subfamily C member 7(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TRPC7 transcript variant 3NM_001167576.1:c.N/AIntron Variant
TRPC7 transcript variant 2NM_001167577.1:c.N/AIntron Variant
TRPC7 transcript variant 1NM_020389.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.279A=0.721
1000GenomesAmericanSub694T=0.240A=0.760
1000GenomesEast AsianSub1008T=0.290A=0.710
1000GenomesEuropeSub1006T=0.347A=0.653
1000GenomesGlobalStudy-wide5008T=0.337A=0.663
1000GenomesSouth AsianSub978T=0.530A=0.470
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.367A=0.633
The Genome Aggregation DatabaseAfricanSub8720T=0.298A=0.702
The Genome Aggregation DatabaseAmericanSub838T=0.270A=0.730
The Genome Aggregation DatabaseEast AsianSub1614T=0.295A=0.705
The Genome Aggregation DatabaseEuropeSub18458T=0.378A=0.621
The Genome Aggregation DatabaseGlobalStudy-wide29932T=0.346A=0.653
The Genome Aggregation DatabaseOtherSub302T=0.250A=0.750
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.312A=0.687
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.361A=0.639
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs25466574.96E-05nicotine dependence17158188

eQTL of rs2546657 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 rs2546657 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 )
chr5135643688135644372E081-39363

Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr5135700942135701290E06817207
chr5135700942135701290E07317207
chr5135700942135701290E08217207