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SNP Detail For rs4420311
1.Mapping Information
| Human SNP ID | rs4420311 |
|---|---|
| Human chromosome | chr12 |
| Human SNP position | 27831257 |
| Pig chromosome | chr5 |
| Pig SNP position | 49470651 |
2.Annotation Information
| PubMed ID | 24945404 |
|---|---|
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24945404 |
| Study | Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. |
| Disease/Trait | Bone mineral density (paediatric, total body less head) |
| Initial sample | 8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children |
| Replication sample | NA |
| Region | 12p11.22 |
| Chromosome id | chr12 |
| Chromosome position | 27831257 |
| Reported gene | KLHDC5, PTHLH |
| Mapped gene | LOC105369709 - PTHLH |
| Upstream gene id | 105369709 |
| Downstream gene id | 5744 |
| SNP gene ids | |
| Upstream gene distance | 7160 |
| Downstream gene distance | 126827 |
| SNP risk allele | rs4420311-G |
| SNPs | rs4420311 |
| Merged | 0 |
| SNP id current | 4420311 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.46 |
| P value | 0.00000004 |
| Pvalue mlog | 7.39794000867203 |
| P value text | |
| Or beta | 0.085 |
| %95 Ci | [0.054-0.116] unit increase |
| Platform | Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST002494 |
| PubMed ID | 24945404 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24945404 |
| Study | Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. |
| Disease/Trait | Bone mineral density (paediatric, total body less head) |
| Initial sample | 8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children |
| Replication sample | NA |
| Region | 12p11.22 |
| Chromosome id | chr12 |
| Chromosome position | 27831257 |
| Reported gene | KLHDC5, PTHLH |
| Mapped gene | LOC105369709 - PTHLH |
| Upstream gene id | 105369709 |
| Downstream gene id | 5744 |
| SNP gene ids | |
| Upstream gene distance | 7160 |
| Downstream gene distance | 126827 |
| SNP risk allele | rs4420311-G |
| SNPs | rs4420311 |
| Merged | 0 |
| SNP id current | 4420311 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 0.0000004 |
| Pvalue mlog | 6.39794000867203 |
| P value text | (EA) |
| Or beta | 0.0872 |
| %95 Ci | [0.053-0.121] unit increase |
| Platform | Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST002494 |
| PubMed ID | 24945404 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24945404 |
| Study | Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. |
| Disease/Trait | Bone mineral density (paediatric, lower limb) |
| Initial sample | 8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children |
| Replication sample | NA |
| Region | 12p11.22 |
| Chromosome id | chr12 |
| Chromosome position | 27831257 |
| Reported gene | KLHDC5, PTHLH |
| Mapped gene | LOC105369709 - PTHLH |
| Upstream gene id | 105369709 |
| Downstream gene id | 5744 |
| SNP gene ids | |
| Upstream gene distance | 7160 |
| Downstream gene distance | 126827 |
| SNP risk allele | rs4420311-G |
| SNPs | rs4420311 |
| Merged | 0 |
| SNP id current | 4420311 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.46 |
| P value | 0.00000003 |
| Pvalue mlog | 7.52287874528033 |
| P value text | |
| Or beta | 0.086 |
| %95 Ci | [0.055-0.117] unit increase |
| Platform | Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST002492 |
| PubMed ID | 24945404 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24945404 |
| Study | Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. |
| Disease/Trait | Bone mineral density (paediatric, lower limb) |
| Initial sample | 8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children |
| Replication sample | NA |
| Region | 12p11.22 |
| Chromosome id | chr12 |
| Chromosome position | 27831257 |
| Reported gene | KLHDC5, PTHLH |
| Mapped gene | LOC105369709 - PTHLH |
| Upstream gene id | 105369709 |
| Downstream gene id | 5744 |
| SNP gene ids | |
| Upstream gene distance | 7160 |
| Downstream gene distance | 126827 |
| SNP risk allele | rs4420311-G |
| SNPs | rs4420311 |
| Merged | 0 |
| SNP id current | 4420311 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 0.0000001 |
| Pvalue mlog | 7 |
| P value text | (EA) |
| Or beta | 0.0921 |
| %95 Ci | [0.058-0.126] unit increase |
| Platform | Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST002492 |
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