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SNP Detail For rs1077989
1.Mapping Information
| Human SNP ID | rs1077989 |
|---|---|
| Human chromosome | chr14 |
| Human SNP position | 67509105 |
| Pig chromosome | chr7 |
| Pig SNP position | 97526832 |
2.Annotation Information
| PubMed ID | 22359512 |
|---|---|
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/22359512 |
| Study | Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. |
| Disease/Trait | Phospholipid levels (plasma) |
| Initial sample | 4,034 European ancestry individuals |
| Replication sample | NA |
| Region | 14q24.1 |
| Chromosome id | chr14 |
| Chromosome position | 67509105 |
| Reported gene | PLEKHH1 |
| Mapped gene | TMEM229B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 161145 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1077989-? |
| SNPs | rs1077989 |
| Merged | 0 |
| SNP id current | 1077989 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000000000000009 |
| Pvalue mlog | 17.0457574905606 |
| P value text | (levels) |
| Or beta | 0 |
| %95 Ci | [0.80-1.80] % increase |
| Platform | Illumina [NR] (imputed) |
| CNV | N |
| Mapped trait | phospholipid measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004639 |
| Study accession | GCST001414 |
| PubMed ID | 26068415 |
| Journal | Nat Commun |
| Link | www.ncbi.nlm.nih.gov/pubmed/26068415 |
| Study | Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. |
| Disease/Trait | Glycerophospholipid levels |
| Initial sample | up to 7,478 European ancestry individuals |
| Replication sample | 1,182 European ancestry individuals |
| Region | 14q24.1 |
| Chromosome id | chr14 |
| Chromosome position | 67509105 |
| Reported gene | TMEM229B |
| Mapped gene | TMEM229B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 161145 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1077989-A |
| SNPs | rs1077989 |
| Merged | 0 |
| SNP id current | 1077989 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.5294 |
| P value | 9E-57 |
| Pvalue mlog | 56.0457574905606 |
| P value text | (Phosphatidylcholine acyl-alkyl C32:1) |
| Or beta | 0.0653 |
| %95 Ci | [0.057-0.073] unit increase |
| Platform | Affymetrix, Illumina [at least 296619] (imputed) |
| CNV | N |
| Mapped trait | glycerophospholipid measurement, blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0007630, http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002965 |
| PubMed ID | 26068415 |
| Journal | Nat Commun |
| Link | www.ncbi.nlm.nih.gov/pubmed/26068415 |
| Study | Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. |
| Disease/Trait | Glycerophospholipid levels |
| Initial sample | up to 7,478 European ancestry individuals |
| Replication sample | 1,182 European ancestry individuals |
| Region | 14q24.1 |
| Chromosome id | chr14 |
| Chromosome position | 67509105 |
| Reported gene | TMEM229B |
| Mapped gene | TMEM229B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 161145 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1077989-A |
| SNPs | rs1077989 |
| Merged | 0 |
| SNP id current | 1077989 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.5292 |
| P value | 1E-45 |
| Pvalue mlog | 45 |
| P value text | (Phosphatidylcholine acyl-alkyl C32:2) |
| Or beta | 0.0603 |
| %95 Ci | [0.052-0.069] unit increase |
| Platform | Affymetrix, Illumina [at least 296619] (imputed) |
| CNV | N |
| Mapped trait | glycerophospholipid measurement, blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0007630, http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002965 |
| PubMed ID | 26068415 |
| Journal | Nat Commun |
| Link | www.ncbi.nlm.nih.gov/pubmed/26068415 |
| Study | Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. |
| Disease/Trait | Glycerophospholipid levels |
| Initial sample | up to 7,478 European ancestry individuals |
| Replication sample | 1,182 European ancestry individuals |
| Region | 14q24.1 |
| Chromosome id | chr14 |
| Chromosome position | 67509105 |
| Reported gene | TMEM229B |
| Mapped gene | TMEM229B |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 161145 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1077989-A |
| SNPs | rs1077989 |
| Merged | 0 |
| SNP id current | 1077989 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.5293 |
| P value | 6E-40 |
| Pvalue mlog | 39.2218487496163 |
| P value text | (Phosphatidylcholine acyl-alkyl C36:5) |
| Or beta | 0.0636 |
| %95 Ci | [0.054-0.073] unit increase |
| Platform | Affymetrix, Illumina [at least 296619] (imputed) |
| CNV | N |
| Mapped trait | glycerophospholipid measurement, blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0007630, http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002965 |
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