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SNP Detail For rs1893217
1.Mapping Information
| Human SNP ID | rs1893217 |
|---|---|
| Human chromosome | chr18 |
| Human SNP position | 12809341 |
| Pig chromosome | chr6 |
| Pig SNP position | 90260536 |
2.Annotation Information
| PubMed ID | 19430480 |
|---|---|
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19430480 |
| Study | Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. |
| Disease/Trait | Type 1 diabetes |
| Initial sample | 7,514 cases, 9,045 controls |
| Replication sample | 4,267 cases, 4,670 controls, 4,342 trios from 2,319 families |
| Region | 18p11.21 |
| Chromosome id | chr18 |
| Chromosome position | 12809341 |
| Reported gene | PTPN2 |
| Mapped gene | PTPN2 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 5771 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1893217-? |
| SNPs | rs1893217 |
| Merged | 0 |
| SNP id current | 1893217 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000000000004 |
| Pvalue mlog | 14.397940008672 |
| P value text | |
| Or beta | |
| %95 Ci | |
| Platform | Affymetrix, Illumina [841622] (imputed) |
| CNV | N |
| Mapped trait | type I diabetes mellitus |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001359 |
| Study accession | GCST000392 |
| PubMed ID | 21383967 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21383967 |
| Study | Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. |
| Disease/Trait | Celiac disease or Rheumatoid arthritis |
| Initial sample | 4,533 European ancestry celiac disease cases, 5,539 European ancestry rheumatoid arthritis cases, 27,981 European ancestry controls |
| Replication sample | 2,169 European ancestry celiac disease cases, 2,845 European ancestry rheumatoid arthritis cases, 7,199 European ancestry controls |
| Region | 18p11.21 |
| Chromosome id | chr18 |
| Chromosome position | 12809341 |
| Reported gene | PTPN2 |
| Mapped gene | PTPN2 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 5771 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1893217-G |
| SNPs | rs1893217 |
| Merged | 0 |
| SNP id current | 1893217 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000000005 |
| Pvalue mlog | 11.3010299956639 |
| P value text | |
| Or beta | |
| %95 Ci | |
| Platform | Illumina [472854] |
| CNV | N |
| Mapped trait | immune system disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000540 |
| Study accession | GCST000987 |
| PubMed ID | 20190752 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20190752 |
| Study | Multiple common variants for celiac disease influencing immune gene expression. |
| Disease/Trait | Celiac disease |
| Initial sample | 4,533 European ancestry cases, 10,750 European ancestry controls |
| Replication sample | 4,918 European ancestry cases, 5,684 European ancestry controls |
| Region | 18p11.21 |
| Chromosome id | chr18 |
| Chromosome position | 12809341 |
| Reported gene | PTPN2 |
| Mapped gene | PTPN2 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 5771 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1893217-G |
| SNPs | rs1893217 |
| Merged | 0 |
| SNP id current | 1893217 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.17 |
| P value | 0.0000000003 |
| Pvalue mlog | 9.52287874528033 |
| P value text | |
| Or beta | 1.17 |
| %95 Ci | [1.12-1.23] |
| Platform | Illumina [292387] |
| CNV | N |
| Mapped trait | celiac disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001060 |
| Study accession | GCST000612 |
| 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 | 18p11.21 |
| Chromosome id | chr18 |
| Chromosome position | 12809341 |
| Reported gene | PTPN2 |
| Mapped gene | PTPN2 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 5771 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1893217-G |
| SNPs | rs1893217 |
| Merged | 0 |
| SNP id current | 1893217 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.153 |
| P value | 0.00000000000001 |
| Pvalue mlog | 14 |
| P value text | |
| Or beta | 1.25 |
| %95 Ci | [1.18-1.32] |
| 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 | 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 | 18p11.21 |
| Chromosome id | chr18 |
| Chromosome position | 12809341 |
| Reported gene | intergenic |
| Mapped gene | PTPN2 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 5771 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1893217-G |
| SNPs | rs1893217 |
| Merged | 0 |
| SNP id current | 1893217 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.157 |
| P value | 3E-26 |
| Pvalue mlog | 25.5228787452803 |
| P value text | |
| Or beta | 1.171 |
| %95 Ci | [1.127-1.216] |
| 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 | 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 | 18p11.21 |
| Chromosome id | chr18 |
| Chromosome position | 12809341 |
| Reported gene | NR |
| Mapped gene | PTPN2 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 5771 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1893217-G |
| SNPs | rs1893217 |
| Merged | 0 |
| SNP id current | 1893217 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.1602 |
| P value | 0.0000000000003 |
| Pvalue mlog | 12.5228787452803 |
| P value text | (EA) |
| Or beta | 1.1283141 |
| %95 Ci | [1.1-1.16] |
| 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 | 18p11.21 |
| Chromosome id | chr18 |
| Chromosome position | 12809341 |
| Reported gene | NR |
| Mapped gene | PTPN2 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 5771 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1893217-G |
| SNPs | rs1893217 |
| Merged | 0 |
| SNP id current | 1893217 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.1602 |
| P value | 6E-25 |
| Pvalue mlog | 24.2218487496163 |
| P value text | (EA) |
| Or beta | 1.1773959 |
| %95 Ci | [1.15-1.21] |
| 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 |
| 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 | Inflammatory bowel disease |
| Initial sample | 12,882 European ancestry cases, 21,770 European ancestry controls |
| Replication sample | 25,273 European ancestry cases, 26,715 European ancestry controls, 548 Iranian ancestry cases, 342 Iranian ancestry control, 1,423 Indian ancestry cases, 990 Indian ancestry controls, 2,824 East Asian ancestry cases, 3,719 East Asian ancestry controls |
| Region | 18p11.21 |
| Chromosome id | chr18 |
| Chromosome position | 12809341 |
| Reported gene | NR |
| Mapped gene | PTPN2 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 5771 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1893217-G |
| SNPs | rs1893217 |
| Merged | 0 |
| SNP id current | 1893217 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.1602 |
| P value | 1E-27 |
| Pvalue mlog | 27 |
| P value text | (EA) |
| Or beta | 1.1539862 |
| %95 Ci | [1.13-1.18] |
| Platform | Affymetrix, Illumina [~ 9000000] (imputed) |
| CNV | N |
| Mapped trait | inflammatory bowel disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003767 |
| Study accession | GCST003043 |
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