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SNP Detail For rs3129882
1.Mapping Information
| Human SNP ID | rs3129882 |
|---|---|
| Human chromosome | chr6 |
| Human SNP position | 32441753 |
| Pig chromosome | chr7 |
| Pig SNP position | 29038033 |
2.Annotation Information
| PubMed ID | 21779181 |
|---|---|
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21779181 |
| Study | Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy. |
| Disease/Trait | Systemic sclerosis |
| Initial sample | 2,296 European ancestry cases, 5,172 European ancestry controls |
| Replication sample | 3,175 European ancestry cases, 4,210 European ancestry controls |
| Region | 6p21.32 |
| Chromosome id | chr6 |
| Chromosome position | 32441753 |
| Reported gene | HLA-DRA |
| Mapped gene | HLA-DRA |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3122 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3129882-? |
| SNPs | rs3129882 |
| Merged | 0 |
| SNP id current | 3129882 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.44 |
| P value | 2E-27 |
| Pvalue mlog | 26.698970004336 |
| P value text | (ATA positive) |
| Or beta | 2.17 |
| %95 Ci | [1.88-2.50] |
| Platform | Illumina [NR] (imputed) |
| CNV | N |
| Mapped trait | systemic scleroderma |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000717 |
| Study accession | GCST001156 |
| PubMed ID | 20711177 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20711177 |
| Study | Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson__s disease. |
| Disease/Trait | Parkinson__s disease |
| Initial sample | 2,000 European ancestry cases, 1,986 European ancestry controls |
| Replication sample | Up to 1,447 cases, 1,468 controls |
| Region | 6p21.32 |
| Chromosome id | chr6 |
| Chromosome position | 32441753 |
| Reported gene | HLA-DRA |
| Mapped gene | HLA-DRA |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3122 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3129882-G |
| SNPs | rs3129882 |
| Merged | 0 |
| SNP id current | 3129882 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.4 |
| P value | 0.0000000002 |
| Pvalue mlog | 9.69897000433601 |
| P value text | |
| Or beta | 1.26 |
| %95 Ci | [1.17-1.35] |
| Platform | Illumina [811597] |
| CNV | N |
| Mapped trait | Parkinson__s disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0002508 |
| Study accession | GCST000772 |
| PubMed ID | 24511991 |
| Journal | BMC Genomics |
| Link | www.ncbi.nlm.nih.gov/pubmed/24511991 |
| Study | Identification of a novel Parkinson__s disease locus via stratified genome-wide association study. |
| Disease/Trait | Parkinson__s disease |
| Initial sample | 1,565 European ancestry sproadic Parkinson__s disease cases, 435 European ancestry familial Parkinson__s disease cases, 1,986 European ancestry controls |
| Replication sample | 1,528 European ancestry sporadic Parkinson__s disease cases, 707 European ancestry familial Parkinson__s disease cases, 796 European ancestry controls |
| Region | 6p21.32 |
| Chromosome id | chr6 |
| Chromosome position | 32441753 |
| Reported gene | HLA |
| Mapped gene | HLA-DRA |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3122 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3129882-G |
| SNPs | rs3129882 |
| Merged | 0 |
| SNP id current | 3129882 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.395 |
| P value | 0.00000003 |
| Pvalue mlog | 7.52287874528033 |
| P value text | |
| Or beta | 1.31 |
| %95 Ci | [1.19-1.43] |
| Platform | Illumina [811597] |
| CNV | N |
| Mapped trait | Parkinson__s disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0002508 |
| Study accession | GCST002353 |
| PubMed ID | 24511991 |
| Journal | BMC Genomics |
| Link | www.ncbi.nlm.nih.gov/pubmed/24511991 |
| Study | Identification of a novel Parkinson__s disease locus via stratified genome-wide association study. |
| Disease/Trait | Parkinson__s disease |
| Initial sample | 1,565 European ancestry sproadic Parkinson__s disease cases, 435 European ancestry familial Parkinson__s disease cases, 1,986 European ancestry controls |
| Replication sample | 1,528 European ancestry sporadic Parkinson__s disease cases, 707 European ancestry familial Parkinson__s disease cases, 796 European ancestry controls |
| Region | 6p21.32 |
| Chromosome id | chr6 |
| Chromosome position | 32441753 |
| Reported gene | HLA |
| Mapped gene | HLA-DRA |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3122 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs3129882-G |
| SNPs | rs3129882 |
| Merged | 0 |
| SNP id current | 3129882 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.395 |
| P value | 0.0000000005 |
| Pvalue mlog | 9.30102999566398 |
| P value text | (Sporadic) |
| Or beta | 1.38 |
| %95 Ci | [1.24-1.52] |
| Platform | Illumina [811597] |
| CNV | N |
| Mapped trait | Parkinson__s disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0002508 |
| Study accession | GCST002353 |
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