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SNP Detail For rs7501939
1.Mapping Information
| Human SNP ID | rs7501939 |
|---|---|
| Human chromosome | chr17 |
| Human SNP position | 37741165 |
| Pig chromosome | chr12 |
| Pig SNP position | 40842818 |
2.Annotation Information
| 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 | 17q12 |
| Chromosome id | chr17 |
| Chromosome position | 37741165 |
| Reported gene | HNF1B |
| Mapped gene | HNF1B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 6928 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs7501939-C |
| SNPs | rs7501939 |
| Merged | 0 |
| SNP id current | 7501939 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.57 |
| P value | 0.000000000009 |
| Pvalue mlog | 11.0457574905606 |
| P value text | |
| Or beta | 1.41 |
| %95 Ci | [NR] |
| 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 | 21743057 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21743057 |
| Study | Genome-wide association study identifies new prostate cancer susceptibility loci. |
| Disease/Trait | Prostate cancer |
| Initial sample | 2,782 European ancestry cases, 4,458 European ancestry controls |
| Replication sample | 7,358 European ancestry cases, 6,732 European ancestry controls |
| Region | 17q12 |
| Chromosome id | chr17 |
| Chromosome position | 37741165 |
| Reported gene | TCF2 |
| Mapped gene | HNF1B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 6928 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs7501939-C |
| SNPs | rs7501939 |
| Merged | 0 |
| SNP id current | 7501939 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000002 |
| Pvalue mlog | 5.69897000433601 |
| P value text | |
| Or beta | 1.19 |
| %95 Ci | [1.11-1.28] |
| Platform | Illumina [571243] |
| CNV | N |
| Mapped trait | prostate carcinoma |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
| Study accession | GCST001147 |
| PubMed ID | 20676098 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20676098 |
| Study | Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population. |
| Disease/Trait | Prostate cancer |
| Initial sample | 1,583 Japanese ancestry cases, 3,386 Japanese ancestry controls |
| Replication sample | 3,001 Japanese ancestry cases, 5,415 Japanese ancestry controls |
| Region | 17q12 |
| Chromosome id | chr17 |
| Chromosome position | 37741165 |
| Reported gene | HNF1B |
| Mapped gene | HNF1B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 6928 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs7501939-? |
| SNPs | rs7501939 |
| Merged | 0 |
| SNP id current | 7501939 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000000001 |
| Pvalue mlog | 12 |
| P value text | |
| Or beta | |
| %95 Ci | |
| Platform | Illumina [510687] |
| CNV | N |
| Mapped trait | prostate carcinoma |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
| Study accession | GCST000750 |
| 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 | 17q12 |
| Chromosome id | chr17 |
| Chromosome position | 37741165 |
| Reported gene | NR |
| Mapped gene | HNF1B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 6928 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs7501939-? |
| SNPs | rs7501939 |
| Merged | 0 |
| SNP id current | 7501939 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000000000000003 |
| Pvalue mlog | 17.5228787452803 |
| 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 | 25877299 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/25877299 |
| Study | Two new loci and gene sets related to sex determination and cancer progression are associated with susceptibility to testicular germ cell tumor. |
| Disease/Trait | Testicular germ cell tumor |
| Initial sample | 1,326 European ancestry cases, 6,687 European ancestry controls |
| Replication sample | 710 European ancestry case-parent triads, 289 European ancestry cases, 290 European ancestry controls |
| Region | 17q12 |
| Chromosome id | chr17 |
| Chromosome position | 37741165 |
| Reported gene | HNF1B |
| Mapped gene | HNF1B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 6928 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs7501939-C |
| SNPs | rs7501939 |
| Merged | 0 |
| SNP id current | 7501939 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.624 |
| P value | 0.000000001 |
| Pvalue mlog | 9 |
| P value text | |
| Or beta | 1.28 |
| %95 Ci | [1.19-1.39] |
| Platform | Illumina [610240] |
| CNV | N |
| Mapped trait | Testicular Germ Cell Tumor |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_1000566 |
| Study accession | GCST002855 |
| PubMed ID | 26034056 |
| Journal | Cancer Discov |
| Link | www.ncbi.nlm.nih.gov/pubmed/26034056 |
| Study | A large multi-ethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences. |
| Disease/Trait | Prostate cancer |
| Initial sample | 6,406 European ancestry cases, 601 African American cases, 288 East Asian ancestry cases, 488 Latino cases30,866 European ancestry controls, 1,650 African American controls, 2,938 East Asian ancestry controls, 3,141 Latino controls |
| Replication sample | 4,599 European ancestry cases, 2,265 African American cases, 2,940 European ancestry controls, 2,414 African American controls |
| Region | 17q12 |
| Chromosome id | chr17 |
| Chromosome position | 37741165 |
| Reported gene | NR |
| Mapped gene | HNF1B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 6928 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs7501939-C |
| SNPs | rs7501939 |
| Merged | 0 |
| SNP id current | 7501939 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.6 |
| P value | 0.00000000000001 |
| Pvalue mlog | 14 |
| P value text | (European) |
| Or beta | 1.19 |
| %95 Ci | [1.14-1.24] |
| Platform | Affymetrix [up to 19977088] (imputed) |
| CNV | N |
| Mapped trait | prostate carcinoma |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
| Study accession | GCST002944 |
| PubMed ID | 26034056 |
| Journal | Cancer Discov |
| Link | www.ncbi.nlm.nih.gov/pubmed/26034056 |
| Study | A large multi-ethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences. |
| Disease/Trait | Prostate cancer |
| Initial sample | 6,406 European ancestry cases, 601 African American cases, 288 East Asian ancestry cases, 488 Latino cases30,866 European ancestry controls, 1,650 African American controls, 2,938 East Asian ancestry controls, 3,141 Latino controls |
| Replication sample | 4,599 European ancestry cases, 2,265 African American cases, 2,940 European ancestry controls, 2,414 African American controls |
| Region | 17q12 |
| Chromosome id | chr17 |
| Chromosome position | 37741165 |
| Reported gene | NR |
| Mapped gene | HNF1B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 6928 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs7501939-C |
| SNPs | rs7501939 |
| Merged | 0 |
| SNP id current | 7501939 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.6 |
| P value | 0.000000000000004 |
| Pvalue mlog | 14.397940008672 |
| P value text | |
| Or beta | 1.17 |
| %95 Ci | [1.13-1.22] |
| Platform | Affymetrix [up to 19977088] (imputed) |
| CNV | N |
| Mapped trait | prostate carcinoma |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
| Study accession | GCST002944 |
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and Xi'an University of Technology ©2014-2017 All Rights Reserved.
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