Human SNP ID | rs6465657 |
---|---|
Human chromosome | chr7 |
Human SNP position | 98187015 |
Pig chromosome | chr3 |
Pig SNP position | 5447326 |
PubMed ID | 18264097 |
---|---|
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/18264097 |
Study | Multiple newly identified loci associated with prostate cancer susceptibility. |
Disease/Trait | Prostate cancer |
Initial sample | 1,854 European ancestry cases, 1,894 European ancestry controls |
Replication sample | 3,268 European ancestry cases, 3,366 European ancestry controls |
Region | 7q21.3 |
Chromosome id | chr7 |
Chromosome position | 98187015 |
Reported gene | LMTK2 |
Mapped gene | LMTK2 |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 22853 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs6465657-C |
SNPs | rs6465657 |
Merged | 0 |
SNP id current | 6465657 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.46 |
P value | 0.000000001 |
Pvalue mlog | 9 |
P value text | |
Or beta | 1.12 |
%95 Ci | [1.05-1.20] |
Platform | Illumina [541129] |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST000152 |
PubMed ID | 19767753 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/19767753 |
Study | Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. |
Disease/Trait | Prostate cancer |
Initial sample | 1,854 European ancestry cases, 1,894 European ancestry controls |
Replication sample | 19,879 cases and 18,761 controls of European, East Asian, African American, Latino, and Hawaiian ancestry |
Region | 7q21.3 |
Chromosome id | chr7 |
Chromosome position | 98187015 |
Reported gene | NR |
Mapped gene | LMTK2 |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 22853 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs6465657-? |
SNPs | rs6465657 |
Merged | 0 |
SNP id current | 6465657 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | NR |
P value | 0.00000002 |
Pvalue mlog | 7.69897000433601 |
P value text | |
Or beta | |
%95 Ci | |
Platform | Illumina [541129] |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST000488 |
PubMed ID | 22219177 |
Journal | Carcinogenesis |
Link | www.ncbi.nlm.nih.gov/pubmed/22219177 |
Study | A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. |
Disease/Trait | Prostate cancer (gene x gene interaction) |
Initial sample | 4,723 European ancestry cases, 4,792 European ancestry controls |
Replication sample | NA |
Region | 16q12.1 x 7q21.3 |
Chromosome id | chr16 x 7 |
Chromosome position | 49360365 x 98187015 |
Reported gene | C16orf78 x LMTK2 |
Mapped gene | LOC105371243 - C16orf78 x LMTK2 |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs8057939-? x rs6465657-? |
SNPs | rs8057939 x rs6465657 |
Merged | 0 |
SNP id current | |
Context | intergenic_variant x intron_variant |
Intergenic | |
Allele frequency | NR |
P value | 0.000005 |
Pvalue mlog | 5.30102999566398 |
P value text | |
Or beta | 1.37 |
%95 Ci | [1.20-1.57] |
Platform | Affymetrix, Illumina [1117531] (imputed) |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST001370 |
PubMed ID | 22219177 |
Journal | Carcinogenesis |
Link | www.ncbi.nlm.nih.gov/pubmed/22219177 |
Study | A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. |
Disease/Trait | Prostate cancer (gene x gene interaction) |
Initial sample | 4,723 European ancestry cases, 4,792 European ancestry controls |
Replication sample | NA |
Region | 3p26.3 x 7q21.3 |
Chromosome id | chr3 x 7 |
Chromosome position | 108303 x 98187015 |
Reported gene | CHL1 x LMTK2 |
Mapped gene | LOC105376920 - LOC101927174 x LMTK2 |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs12485321-? x rs6465657-? |
SNPs | rs12485321 x rs6465657 |
Merged | 0 |
SNP id current | |
Context | intergenic_variant x intron_variant |
Intergenic | |
Allele frequency | NR |
P value | 0.000003 |
Pvalue mlog | 5.52287874528033 |
P value text | |
Or beta | 1.2346 |
%95 Ci | [1.14-1.35] |
Platform | Affymetrix, Illumina [1117531] (imputed) |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST001370 |