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SNP Detail For rs1900004
1.Mapping Information
| Human SNP ID | rs1900004 |
|---|---|
| Human chromosome | chr10 |
| Human SNP position | 68241124 |
| Pig chromosome | chr14 |
| Pig SNP position | 77471149 |
2.Annotation Information
| PubMed ID | 20548946 |
|---|---|
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20548946 |
| Study | A genome-wide association study of optic disc parameters. |
| Disease/Trait | Vertical cup-disc ratio |
| Initial sample | 7,360 European ancestry individuals |
| Replication sample | 4,455 European ancestry individuals |
| Region | 10q21.3 |
| Chromosome id | chr10 |
| Chromosome position | 68241124 |
| Reported gene | ATOH7, PBLD |
| Mapped gene | ATOH7 - PBLD |
| Upstream gene id | 220202 |
| Downstream gene id | 64081 |
| SNP gene ids | |
| Upstream gene distance | 9011 |
| Downstream gene distance | 41536 |
| SNP risk allele | rs1900004-T |
| SNPs | rs1900004 |
| Merged | 0 |
| SNP id current | 1900004 |
| Context | intron_variant |
| Intergenic | 1 |
| Allele frequency | 0.22 |
| P value | 0.00000002 |
| Pvalue mlog | 7.69897000433601 |
| P value text | |
| Or beta | 0.01 |
| %95 Ci | [0.009-0.017] mm2 decrease |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | optic disc size measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004832 |
| Study accession | GCST000700 |
| PubMed ID | 20548946 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20548946 |
| Study | A genome-wide association study of optic disc parameters. |
| Disease/Trait | Optic disc parameters |
| Initial sample | 7,360 European ancestry individuals |
| Replication sample | 4,455 European ancestry individuals |
| Region | 10q21.3 |
| Chromosome id | chr10 |
| Chromosome position | 68241124 |
| Reported gene | ATOH7, PBLD |
| Mapped gene | ATOH7 - PBLD |
| Upstream gene id | 220202 |
| Downstream gene id | 64081 |
| SNP gene ids | |
| Upstream gene distance | 9011 |
| Downstream gene distance | 41536 |
| SNP risk allele | rs1900004-T |
| SNPs | rs1900004 |
| Merged | 0 |
| SNP id current | 1900004 |
| Context | intron_variant |
| Intergenic | 1 |
| Allele frequency | 0.22 |
| P value | 3E-35 |
| Pvalue mlog | 34.5228787452803 |
| P value text | |
| Or beta | 0.07 |
| %95 Ci | [0.06-0.08] mm decrease |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | optic disc size measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004832 |
| Study accession | GCST000699 |
| PubMed ID | 25631615 |
| Journal | Genet Epidemiol |
| Link | www.ncbi.nlm.nih.gov/pubmed/25631615 |
| Study | Meta-analysis of Genome-Wide Association Studies Identifies Novel Loci Associated With Optic Disc Morphology. |
| Disease/Trait | Optic disc area |
| Initial sample | 15,117 European ancestry individuals, 2,131 Erasmus Rucphen Family individuals |
| Replication sample | 2,405 Chinese ancestry individuals, 2,305 Malay ancestry individuals, 2,131 Indian ancestry individuals |
| Region | 10q21.3 |
| Chromosome id | chr10 |
| Chromosome position | 68241124 |
| Reported gene | ATOH7 |
| Mapped gene | ATOH7 - PBLD |
| Upstream gene id | 220202 |
| Downstream gene id | 64081 |
| SNP gene ids | |
| Upstream gene distance | 9011 |
| Downstream gene distance | 41536 |
| SNP risk allele | rs1900004-T |
| SNPs | rs1900004 |
| Merged | 0 |
| SNP id current | 1900004 |
| Context | intron_variant |
| Intergenic | 1 |
| Allele frequency | 0.23 |
| P value | 1E-73 |
| Pvalue mlog | 73 |
| P value text | |
| Or beta | 0.097 |
| %95 Ci | [0.087-0.107] unit decrease |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | optic disc area measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0006937 |
| Study accession | GCST002765 |
| PubMed ID | 25631615 |
| Journal | Genet Epidemiol |
| Link | www.ncbi.nlm.nih.gov/pubmed/25631615 |
| Study | Meta-analysis of Genome-Wide Association Studies Identifies Novel Loci Associated With Optic Disc Morphology. |
| Disease/Trait | Optic disc area |
| Initial sample | 15,117 European ancestry individuals, 2,131 Erasmus Rucphen Family individuals |
| Replication sample | 2,405 Chinese ancestry individuals, 2,305 Malay ancestry individuals, 2,131 Indian ancestry individuals |
| Region | 10q21.3 |
| Chromosome id | chr10 |
| Chromosome position | 68241124 |
| Reported gene | ATOH7 |
| Mapped gene | ATOH7 - PBLD |
| Upstream gene id | 220202 |
| Downstream gene id | 64081 |
| SNP gene ids | |
| Upstream gene distance | 9011 |
| Downstream gene distance | 41536 |
| SNP risk allele | rs1900004-T |
| SNPs | rs1900004 |
| Merged | 0 |
| SNP id current | 1900004 |
| Context | intron_variant |
| Intergenic | 1 |
| Allele frequency | 0.23 |
| P value | 2E-63 |
| Pvalue mlog | 62.698970004336 |
| P value text | (EA) |
| Or beta | 0.102 |
| %95 Ci | [0.090-0.114] unit decrease |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | optic disc area measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0006937 |
| Study accession | GCST002765 |
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