PigVar
Overview
Pig SNPs
SNP Table
SNP Hit on Gene
SNP Coding
SNP lincRNA
Search SNPs by Region
Browse on Chromosome
SV
Positive Selection
Help
Manual
Pipeline
Data Statistics
Contact Us
Download
SNP Detail For rs6677604
1.Mapping Information
| Human SNP ID | rs6677604 |
|---|---|
| Human chromosome | chr1 |
| Human SNP position | 196717788 |
| Pig chromosome | chr10 |
| Pig SNP position | 24389576 |
2.Annotation Information
| PubMed ID | 21399633 |
|---|---|
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21399633 |
| Study | Genome-wide association study identifies susceptibility loci for IgA nephropathy. |
| Disease/Trait | Nephropathy |
| Initial sample | 1,194 Han Chinese ancestry cases, 902 Han Chinese ancestry controls |
| Replication sample | 712 Han Chinese ancestry cases, 748 Han Chinese ancestry controls, 1,238 European ancestry cases, 1,172 European ancestry controls |
| Region | 1q31.3 |
| Chromosome id | chr1 |
| Chromosome position | 196717788 |
| Reported gene | CFHR1, CFHR4, CHFR2, CFHR3, CFHR5, CFH |
| Mapped gene | CFH |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3075 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6677604-? |
| SNPs | rs6677604 |
| Merged | 0 |
| SNP id current | 6677604 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.77 (EA) |
| P value | 0.0000000003 |
| Pvalue mlog | 9.52287874528033 |
| P value text | |
| Or beta | 1.47 |
| %95 Ci | [NR] |
| Platform | Illumina [498322] |
| CNV | N |
| Mapped trait | kidney disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003086 |
| Study accession | GCST001009 |
| PubMed ID | 25305756 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/25305756 |
| Study | Discovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens. |
| Disease/Trait | IgA nephropathy |
| Initial sample | 1,194 Han Chinese ancestry cases, 902 Han Chinese ancestry controls, 1,553 European ancestry cases, 3,050 European ancestry controls |
| Replication sample | 2,491 East Asian ancestry cases, 1,780 East Asian ancestry controls, 2,420 European ancestry cases, 7,222 European ancestry controls |
| Region | 1q31.3 |
| Chromosome id | chr1 |
| Chromosome position | 196717788 |
| Reported gene | CFHR3, CFHR1 |
| Mapped gene | CFH |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3075 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6677604-G |
| SNPs | rs6677604 |
| Merged | 0 |
| SNP id current | 6677604 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.8 |
| P value | 0.00000000000005 |
| Pvalue mlog | 13.3010299956639 |
| P value text | |
| Or beta | 1.35 |
| %95 Ci | [NR] |
| Platform | Illumina [> 1000000] (imputed) |
| CNV | N |
| Mapped trait | IGA glomerulonephritis |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004194 |
| Study accession | GCST002655 |
| PubMed ID | 25305756 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/25305756 |
| Study | Discovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens. |
| Disease/Trait | IgA nephropathy |
| Initial sample | 1,194 Han Chinese ancestry cases, 902 Han Chinese ancestry controls, 1,553 European ancestry cases, 3,050 European ancestry controls |
| Replication sample | 2,491 East Asian ancestry cases, 1,780 East Asian ancestry controls, 2,420 European ancestry cases, 7,222 European ancestry controls |
| Region | 1q31.3 |
| Chromosome id | chr1 |
| Chromosome position | 196717788 |
| Reported gene | CFHR3 |
| Mapped gene | CFH |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3075 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6677604-G |
| SNPs | rs6677604 |
| Merged | 0 |
| SNP id current | 6677604 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.8 |
| P value | 0.000000002 |
| Pvalue mlog | 8.69897000433601 |
| P value text | (EA) |
| Or beta | 1.3 |
| %95 Ci | [NR] |
| Platform | Illumina [> 1000000] (imputed) |
| CNV | N |
| Mapped trait | IGA glomerulonephritis |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004194 |
| Study accession | GCST002655 |
| PubMed ID | 25305756 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/25305756 |
| Study | Discovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens. |
| Disease/Trait | IgA nephropathy |
| Initial sample | 1,194 Han Chinese ancestry cases, 902 Han Chinese ancestry controls, 1,553 European ancestry cases, 3,050 European ancestry controls |
| Replication sample | 2,491 East Asian ancestry cases, 1,780 East Asian ancestry controls, 2,420 European ancestry cases, 7,222 European ancestry controls |
| Region | 1q31.3 |
| Chromosome id | chr1 |
| Chromosome position | 196717788 |
| Reported gene | CFHR3 |
| Mapped gene | CFH |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3075 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6677604-G |
| SNPs | rs6677604 |
| Merged | 0 |
| SNP id current | 6677604 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.93 |
| P value | 0.0000007 |
| Pvalue mlog | 6.15490195998574 |
| P value text | (East Asian) |
| Or beta | 1.57 |
| %95 Ci | [NR] |
| Platform | Illumina [> 1000000] (imputed) |
| CNV | N |
| Mapped trait | IGA glomerulonephritis |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004194 |
| Study accession | GCST002655 |
|
Kunming Institute of Zoology, CAS
and Xi'an University of Technology ©2014-2017 All Rights Reserved.
|
|