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SNP Detail For rs10896449
1.Mapping Information
| Human SNP ID | rs10896449 |
|---|---|
| Human chromosome | chr11 |
| Human SNP position | 69227200 |
| Pig chromosome | chr2 |
| Pig SNP position | 2623859 |
2.Annotation Information
| PubMed ID | 18264096 |
|---|---|
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/18264096 |
| Study | Multiple loci identified in a genome-wide association study of prostate cancer. |
| Disease/Trait | Prostate cancer |
| Initial sample | 1,172 European ancestry cases, 1,157 European ancestry controls |
| Replication sample | 3,941 European ancestry cases, 3,964 European ancestry controls |
| Region | 11q13.3 |
| Chromosome id | chr11 |
| Chromosome position | 69227200 |
| Reported gene | intergenic |
| Mapped gene | LOC105369366 - LOC105369367 |
| Upstream gene id | 105369366 |
| Downstream gene id | 105369367 |
| SNP gene ids | |
| Upstream gene distance | 49224 |
| Downstream gene distance | 1549 |
| SNP risk allele | rs10896449-G |
| SNPs | rs10896449 |
| Merged | 0 |
| SNP id current | 10896449 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.52 |
| P value | 0.000000002 |
| Pvalue mlog | 8.69897000433601 |
| P value text | |
| Or beta | 1.1 |
| %95 Ci | [0.98-1.23] |
| Platform | Illumina [527869] |
| CNV | N |
| Mapped trait | prostate carcinoma |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
| Study accession | GCST000154 |
| 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 | 11q13.3 |
| Chromosome id | chr11 |
| Chromosome position | 69227200 |
| Reported gene | NR |
| Mapped gene | LOC105369366 - LOC105369367 |
| Upstream gene id | 105369366 |
| Downstream gene id | 105369367 |
| SNP gene ids | |
| Upstream gene distance | 49224 |
| Downstream gene distance | 1549 |
| SNP risk allele | rs10896449-G |
| SNPs | rs10896449 |
| Merged | 0 |
| SNP id current | 10896449 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.52 |
| P value | 0.000000000000000008 |
| Pvalue mlog | 17.096910013008 |
| P value text | (European) |
| Or beta | 1.21 |
| %95 Ci | [1.16-1.26] |
| 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 | 11q13.3 |
| Chromosome id | chr11 |
| Chromosome position | 69227200 |
| Reported gene | NR |
| Mapped gene | LOC105369366 - LOC105369367 |
| Upstream gene id | 105369366 |
| Downstream gene id | 105369367 |
| SNP gene ids | |
| Upstream gene distance | 49224 |
| Downstream gene distance | 1549 |
| SNP risk allele | rs10896449-G |
| SNPs | rs10896449 |
| Merged | 0 |
| SNP id current | 10896449 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.52 |
| P value | 5E-19 |
| Pvalue mlog | 18.3010299956639 |
| P value text | |
| Or beta | 1.2 |
| %95 Ci | [1.15-1.24] |
| 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 | 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 | 2q33.1 x 11q13.3 |
| Chromosome id | chr2 x 11 |
| Chromosome position | 198304372 x 69227200 |
| Reported gene | PLCL1 x MYEOV |
| Mapped gene | LOC101927619 x LOC105369366 - LOC105369367 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13398206-? x rs10896449-? |
| SNPs | rs13398206 x rs10896449 |
| Merged | 0 |
| SNP id current | |
| Context | intron_variant x intergenic_variant |
| Intergenic | |
| Allele frequency | NR |
| P value | 0.000004 |
| Pvalue mlog | 5.39794000867203 |
| P value text | |
| Or beta | 1.24 |
| %95 Ci | [1.13-1.36] |
| 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 |
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