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SNP Detail For rs3858145
1.Mapping Information
| Human SNP ID | rs3858145 |
|---|---|
| Human chromosome | chr10 |
| Human SNP position | 68252081 |
| Pig chromosome | chr14 |
| Pig SNP position | 77479006 |
2.Annotation Information
| PubMed ID | 20395239 |
|---|---|
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20395239 |
| Study | Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. |
| Disease/Trait | Optic nerve measurement (disc area) |
| Initial sample | 1,368 European ancestry twins from 666 families |
| Replication sample | 848 European ancestry twins from 531 families |
| Region | 10q21.3 |
| Chromosome id | chr10 |
| Chromosome position | 68252081 |
| Reported gene | ATOH7 |
| Mapped gene | ATOH7 - PBLD |
| Upstream gene id | 220202 |
| Downstream gene id | 64081 |
| SNP gene ids | |
| Upstream gene distance | 19968 |
| Downstream gene distance | 30579 |
| SNP risk allele | rs3858145-A |
| SNPs | rs3858145 |
| Merged | 0 |
| SNP id current | 3858145 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 0.0000000003 |
| Pvalue mlog | 9.52287874528033 |
| P value text | |
| Or beta | 0.295 |
| %95 Ci | [0.20-0.39] unit increase |
| Platform | Illumina [~ 2740000] (imputed) |
| CNV | N |
| Mapped trait | optic disc size measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004832 |
| Study accession | GCST000657 |
| PubMed ID | 20395239 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20395239 |
| Study | Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. |
| Disease/Trait | Optic nerve measurement (cup area) |
| Initial sample | 1,368 European ancestry twins from 666 families |
| Replication sample | 848 European ancestry twins from 531 families |
| Region | 10q21.3 |
| Chromosome id | chr10 |
| Chromosome position | 68252081 |
| Reported gene | ATOH7 |
| Mapped gene | ATOH7 - PBLD |
| Upstream gene id | 220202 |
| Downstream gene id | 64081 |
| SNP gene ids | |
| Upstream gene distance | 19968 |
| Downstream gene distance | 30579 |
| SNP risk allele | rs3858145-A |
| SNPs | rs3858145 |
| Merged | 0 |
| SNP id current | 3858145 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 0.0000002 |
| Pvalue mlog | 6.69897000433601 |
| P value text | |
| Or beta | 0.209 |
| %95 Ci | [0.11-0.30] unit increase |
| Platform | Illumina [~ 2740000] (imputed) |
| CNV | N |
| Mapped trait | optic disc size measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004832 |
| Study accession | GCST000659 |
| 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 cup area |
| Initial sample | 15,087 European ancestry individuals, 2,131 Erasmus Rucphen Family individuals |
| Replication sample | 2,363 Chinese ancestry individuals, 2,225 Malay ancestry individuals, 2,025 Indian ancestry individuals |
| Region | 10q21.3 |
| Chromosome id | chr10 |
| Chromosome position | 68252081 |
| Reported gene | ATOH7 |
| Mapped gene | ATOH7 - PBLD |
| Upstream gene id | 220202 |
| Downstream gene id | 64081 |
| SNP gene ids | |
| Upstream gene distance | 19968 |
| Downstream gene distance | 30579 |
| SNP risk allele | rs3858145-G |
| SNPs | rs3858145 |
| Merged | 0 |
| SNP id current | 3858145 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.25 |
| P value | 0.00000008 |
| Pvalue mlog | 7.09691001300805 |
| P value text | |
| Or beta | 0.015 |
| %95 Ci | [0.0091-0.0209] unit decrease |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | optic cup area measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0006940 |
| Study accession | GCST002762 |
| 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 cup area |
| Initial sample | 15,087 European ancestry individuals, 2,131 Erasmus Rucphen Family individuals |
| Replication sample | 2,363 Chinese ancestry individuals, 2,225 Malay ancestry individuals, 2,025 Indian ancestry individuals |
| Region | 10q21.3 |
| Chromosome id | chr10 |
| Chromosome position | 68252081 |
| Reported gene | ATOH7 |
| Mapped gene | ATOH7 - PBLD |
| Upstream gene id | 220202 |
| Downstream gene id | 64081 |
| SNP gene ids | |
| Upstream gene distance | 19968 |
| Downstream gene distance | 30579 |
| SNP risk allele | rs3858145-G |
| SNPs | rs3858145 |
| Merged | 0 |
| SNP id current | 3858145 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.25 |
| P value | 0.0000000004 |
| Pvalue mlog | 9.39794000867203 |
| P value text | (EA) |
| Or beta | 0.019 |
| %95 Ci | [0.013-0.025] unit decrease |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | optic cup area measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0006940 |
| Study accession | GCST002762 |
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