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SNP Detail For rs3197999
1.Mapping Information
| Human SNP ID | rs3197999 |
|---|---|
| Human chromosome | chr3 |
| Human SNP position | 49684099 |
| Pig chromosome | chr13 |
| Pig SNP position | 35394278 |
2.Annotation Information
| PubMed ID | 18587394 |
|---|---|
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/18587394 |
| Study | Genome-wide association defines more than 30 distinct susceptibility loci for Crohn__s disease. |
| Disease/Trait | Crohn__s disease |
| Initial sample | 3,230 European ancestry cases, 4,829 European ancestry controls |
| Replication sample | 1,339 European ancestry trios, 2,325 European ancestry cases, 1,809 European ancestry controls |
| Region | 3p21.31 |
| Chromosome id | chr3 |
| Chromosome position | 49684099 |
| Reported gene | MST1 |
| Mapped gene | MST1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 4485 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3197999-A |
| SNPs | rs3197999 |
| Merged | 0 |
| SNP id current | 3197999 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.27 |
| P value | 0.000000000001 |
| Pvalue mlog | 12 |
| P value text | |
| Or beta | 1.2 |
| %95 Ci | [NR] |
| Platform | Affymetrix, Illumina [635547] (imputed) |
| CNV | N |
| Mapped trait | Crohn__s disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000384 |
| Study accession | GCST000207 |
| PubMed ID | 21151127 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21151127 |
| Study | Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci. |
| Disease/Trait | Primary sclerosing cholangitis |
| Initial sample | 715 European ancestry cases, 2,962 European ancestry controls |
| Replication sample | 1,025 European ancestry cases, 2,174 European ancestry controls |
| Region | 3p21.31 |
| Chromosome id | chr3 |
| Chromosome position | 49684099 |
| Reported gene | MST1 |
| Mapped gene | MST1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 4485 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3197999-? |
| SNPs | rs3197999 |
| Merged | 0 |
| SNP id current | 3197999 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.28 |
| P value | 0.0000000000000001 |
| Pvalue mlog | 16 |
| P value text | |
| Or beta | 1.39 |
| %95 Ci | [1.24-1.56] |
| Platform | Affymetrix [2466182] (imputed) |
| CNV | N |
| Mapped trait | sclerosing cholangitis |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004268 |
| Study accession | GCST000915 |
| PubMed ID | 21102463 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21102463 |
| Study | Genome-wide meta-analysis increases to 71 the number of confirmed Crohn__s disease susceptibility loci. |
| Disease/Trait | Crohn__s disease |
| Initial sample | 6,333 European ancestry cases, 15,056 European ancestry controls |
| Replication sample | 15,694 European ancestry cases, 14,026 European ancestry controls, 414 European ancestry trios |
| Region | 3p21.31 |
| Chromosome id | chr3 |
| Chromosome position | 49684099 |
| Reported gene | MST1, GPX1, BSN |
| Mapped gene | MST1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 4485 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3197999-A |
| SNPs | rs3197999 |
| Merged | 0 |
| SNP id current | 3197999 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.297 |
| P value | 0.00000000000000006 |
| Pvalue mlog | 16.2218487496163 |
| P value text | |
| Or beta | 1.22 |
| %95 Ci | [1.16-1.27] |
| Platform | Affymetrix, Illumina [953241] (imputed) |
| CNV | N |
| Mapped trait | Crohn__s disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000384 |
| Study accession | GCST000879 |
| PubMed ID | 25082827 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/25082827 |
| Study | A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis. |
| Disease/Trait | Ulcerative colitis |
| Initial sample | up to 7,483 European ancestry cases, up to 21,211 European ancestry controls |
| Replication sample | 1,073 European ancestry cases, 1,279 European ancestry controls |
| Region | 3p21.31 |
| Chromosome id | chr3 |
| Chromosome position | 49684099 |
| Reported gene | PFKFB4, MST1R, UCN2, GPX1, IP6K2, BSN, IP6K1, USP4, MST1 |
| Mapped gene | MST1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 4485 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3197999-? |
| SNPs | rs3197999 |
| Merged | 0 |
| SNP id current | 3197999 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.0000008 |
| Pvalue mlog | 6.09691001300805 |
| P value text | (Southern European) |
| Or beta | 1.38 |
| %95 Ci | [1.21-1.56] |
| Platform | Illumina [546271] |
| CNV | N |
| Mapped trait | ulcerative colitis |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000729 |
| Study accession | GCST002548 |
| PubMed ID | 23128233 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/23128233 |
| Study | Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. |
| Disease/Trait | Inflammatory bowel disease |
| Initial sample | 12,924 European ancestry cases, 21,442 European ancestry controls |
| Replication sample | 25,683 European ancestry cases, 17,015 European ancestry controls |
| Region | 3p21.31 |
| Chromosome id | chr3 |
| Chromosome position | 49684099 |
| Reported gene | PFKFB4, MST1R, UCN2, IP6K2, MST1, IP6K1, GPX1, USP4, BSN |
| Mapped gene | MST1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 4485 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3197999-A |
| SNPs | rs3197999 |
| Merged | 0 |
| SNP id current | 3197999 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.296 |
| P value | 1E-47 |
| Pvalue mlog | 47 |
| P value text | |
| Or beta | 1.18 |
| %95 Ci | [1.144-1.216] |
| Platform | Affymetrix, Illumina [1230000] (imputed) |
| CNV | N |
| Mapped trait | inflammatory bowel disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003767 |
| Study accession | GCST001725 |
| PubMed ID | 20228799 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20228799 |
| Study | Genome-wide association identifies multiple ulcerative colitis susceptibility loci. |
| Disease/Trait | Ulcerative colitis |
| Initial sample | 2,693 European ancestry cases, 6,791 European ancestry controls |
| Replication sample | 2,009 European ancestry cases, 1,580 European ancestry controls |
| Region | 3p21.31 |
| Chromosome id | chr3 |
| Chromosome position | 49684099 |
| Reported gene | MST1 |
| Mapped gene | MST1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 4485 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3197999-T |
| SNPs | rs3197999 |
| Merged | 0 |
| SNP id current | 3197999 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000004 |
| Pvalue mlog | 8.39794000867203 |
| P value text | |
| Or beta | 1.21 |
| %95 Ci | [NR] |
| Platform | Illumina [266047] |
| CNV | N |
| Mapped trait | ulcerative colitis |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000729 |
| Study accession | GCST000624 |
| PubMed ID | 26192919 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26192919 |
| Study | Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. |
| Disease/Trait | Ulcerative colitis |
| Initial sample | 6,968 European ancestry cases, 20,464 European ancestry controls |
| Replication sample | 10,679 European ancestry cases, 26,715 European ancestry controls, 397 Iranian ancestry cases, 342 Iranian ancestry controls, 1,239 Indian ancestry cases, 990 Indian ancestry controls, 1,134 East Asian ancestry cases, 3,719 East Asian ancestry controls |
| Region | 3p21.31 |
| Chromosome id | chr3 |
| Chromosome position | 49684099 |
| Reported gene | NR |
| Mapped gene | MST1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 4485 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3197999-A |
| SNPs | rs3197999 |
| Merged | 0 |
| SNP id current | 3197999 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.2812 |
| P value | 2E-37 |
| Pvalue mlog | 36.698970004336 |
| P value text | (EA) |
| Or beta | 1.1865767 |
| %95 Ci | [1.16-1.21] |
| Platform | Affymetrix, Illumina [~ 9000000] (imputed) |
| CNV | N |
| Mapped trait | ulcerative colitis |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000729 |
| Study accession | GCST003045 |
| PubMed ID | 26192919 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26192919 |
| Study | Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. |
| Disease/Trait | Crohn__s disease |
| Initial sample | 5,956 European ancestry cases, 14,927 European ancestry controls |
| Replication sample | 14,594 European ancestry cases, 26,715 European ancestry controls, 151 Iranian ancestry cases, 342 Iranian ancestry controls, 184 Indian ancestry cases, 990 Indian ancestry controls, 1,690 East Asian ancestry cases, 3,719 East Asian ancestry controls |
| Region | 3p21.31 |
| Chromosome id | chr3 |
| Chromosome position | 49684099 |
| Reported gene | NR |
| Mapped gene | MST1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 4485 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3197999-A |
| SNPs | rs3197999 |
| Merged | 0 |
| SNP id current | 3197999 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.2812 |
| P value | 2E-33 |
| Pvalue mlog | 32.698970004336 |
| P value text | (EA) |
| Or beta | 1.1677914 |
| %95 Ci | [1.14-1.19] |
| Platform | Affymetrix, Illumina [~ 9000000] (imputed) |
| CNV | N |
| Mapped trait | Crohn__s disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000384 |
| Study accession | GCST003044 |
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and Xi'an University of Technology ©2014-2017 All Rights Reserved.
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