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SNP Detail For rs2304130
1.Mapping Information
| Human SNP ID | rs2304130 |
|---|---|
| Human chromosome | chr19 |
| Human SNP position | 19678719 |
| Pig chromosome | chr2 |
| Pig SNP position | 66779159 |
2.Annotation Information
| PubMed ID | 19060911 |
|---|---|
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19060911 |
| Study | Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. |
| Disease/Trait | Triglycerides |
| Initial sample | 17,100 European ancestry individuals, 715 Orcadian individuals |
| Replication sample | NA |
| Region | 19p13.11 |
| Chromosome id | chr19 |
| Chromosome position | 19678719 |
| Reported gene | NCAN |
| Mapped gene | ZNF101 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 94039 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2304130-G |
| SNPs | rs2304130 |
| Merged | 0 |
| SNP id current | 2304130 |
| Context | splice_region_variant |
| Intergenic | 0 |
| Allele frequency | 0.07 |
| P value | 0.000003 |
| Pvalue mlog | 5.52287874528033 |
| P value text | |
| Or beta | 0.1 |
| %95 Ci | [NR] s.d. decrease |
| Platform | Affymetrix, Illumina [up to 600000] |
| CNV | N |
| Mapped trait | triglyceride measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004530 |
| Study accession | GCST000289 |
| PubMed ID | 19060911 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19060911 |
| Study | Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. |
| Disease/Trait | LDL cholesterol |
| Initial sample | 17,083 European ancestry individuals, 714 Orcadian individuals |
| Replication sample | NA |
| Region | 19p13.11 |
| Chromosome id | chr19 |
| Chromosome position | 19678719 |
| Reported gene | NCAN |
| Mapped gene | ZNF101 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 94039 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2304130-G |
| SNPs | rs2304130 |
| Merged | 0 |
| SNP id current | 2304130 |
| Context | splice_region_variant |
| Intergenic | 0 |
| Allele frequency | 0.07 |
| P value | 0.000003 |
| Pvalue mlog | 5.52287874528033 |
| P value text | |
| Or beta | 0.12 |
| %95 Ci | [NR] s.d. decrease |
| Platform | Affymetrix, Illumina [up to 600000] |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST000282 |
| PubMed ID | 19060911 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19060911 |
| Study | Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. |
| Disease/Trait | Cholesterol, total |
| Initial sample | 21,848 European ancestry individuals, 714 Orcadian individuals |
| Replication sample | NA |
| Region | 19p13.11 |
| Chromosome id | chr19 |
| Chromosome position | 19678719 |
| Reported gene | NCAN |
| Mapped gene | ZNF101 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 94039 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2304130-G |
| SNPs | rs2304130 |
| Merged | 0 |
| SNP id current | 2304130 |
| Context | splice_region_variant |
| Intergenic | 0 |
| Allele frequency | 0.07 |
| P value | 0.000000000000002 |
| Pvalue mlog | 14.698970004336 |
| P value text | |
| Or beta | 0.15 |
| %95 Ci | [NR] s.d. decrease |
| Platform | Affymetrix, Illumina [up to 600000] |
| CNV | N |
| Mapped trait | total cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004574 |
| Study accession | GCST000285 |
| PubMed ID | 20864672 |
| Journal | Arterioscler Thromb Vasc Biol |
| Link | www.ncbi.nlm.nih.gov/pubmed/20864672 |
| Study | Genetic variants influencing circulating lipid levels and risk of coronary artery disease. |
| Disease/Trait | Triglycerides |
| Initial sample | up to 17,723 European ancestry individuals |
| Replication sample | up to 37,774 European ancestry individuals, up to 9,665 Indian Asian ancestry individuals |
| Region | 19p13.11 |
| Chromosome id | chr19 |
| Chromosome position | 19678719 |
| Reported gene | CILP2, ZNF101 |
| Mapped gene | ZNF101 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 94039 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2304130-G |
| SNPs | rs2304130 |
| Merged | 0 |
| SNP id current | 2304130 |
| Context | splice_region_variant |
| Intergenic | 0 |
| Allele frequency | 0.09 |
| P value | 0.00000004 |
| Pvalue mlog | 7.39794000867203 |
| P value text | |
| Or beta | 0.07 |
| %95 Ci | [0.04-0.10] unit decrease |
| Platform | Affymetrix, Illumina, Perlegen [2155369] (imputed) |
| CNV | N |
| Mapped trait | triglyceride measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004530 |
| Study accession | GCST000809 |
| 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 | Sphingolipid levels |
| Initial sample | 4,034 European ancestry individuals |
| Replication sample | NA |
| Region | 19p13.11 |
| Chromosome id | chr19 |
| Chromosome position | 19678719 |
| Reported gene | LPAR2 |
| Mapped gene | ZNF101 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 94039 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2304130-? |
| SNPs | rs2304130 |
| Merged | 0 |
| SNP id current | 2304130 |
| Context | splice_region_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000006 |
| Pvalue mlog | 8.22184874961635 |
| P value text | (proportions) |
| Or beta | 0.8 |
| %95 Ci | [NR] % increase |
| Platform | Illumina [NR] (imputed) |
| CNV | N |
| Mapped trait | sphingolipid measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004622 |
| Study accession | GCST001413 |
| PubMed ID | 25673413 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/25673413 |
| Study | Genetic studies of body mass index yield new insights for obesity biology. |
| Disease/Trait | Body mass index |
| Initial sample | up to 104,666 European ancestry male individuals, up to 132,115 European ancestry female individuals, 370 African American male individuals, 517 African American female individuals, 512 Hispanic male individuals, 764 Hispanic female individuals |
| Replication sample | up to 48,274 European ancestry male individuals, up to 39,864 European ancestry female individuals, 2,441 African American or Afro-Caribbean male individuals, 6,314 African American or Afro-Caribbean female individuals, 919 Filipino male individuals, 828 |
| Region | 19p13.11 |
| Chromosome id | chr19 |
| Chromosome position | 19678719 |
| Reported gene | ZNF101 |
| Mapped gene | ZNF101 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 94039 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2304130-A |
| SNPs | rs2304130 |
| Merged | 0 |
| SNP id current | 2304130 |
| Context | splice_region_variant |
| Intergenic | 0 |
| Allele frequency | 0.914 |
| P value | 0.000005 |
| Pvalue mlog | 5.30102999566398 |
| P value text | (EA) |
| Or beta | 0.027 |
| %95 Ci | [0.015-0.038] kg/m2 increase |
| Platform | Affymetrix, Illumina [2550021] |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST002783 |
| PubMed ID | 25673413 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/25673413 |
| Study | Genetic studies of body mass index yield new insights for obesity biology. |
| Disease/Trait | Body mass index |
| Initial sample | up to 104,666 European ancestry male individuals, up to 132,115 European ancestry female individuals, 370 African American male individuals, 517 African American female individuals, 512 Hispanic male individuals, 764 Hispanic female individuals |
| Replication sample | up to 48,274 European ancestry male individuals, up to 39,864 European ancestry female individuals, 2,441 African American or Afro-Caribbean male individuals, 6,314 African American or Afro-Caribbean female individuals, 919 Filipino male individuals, 828 |
| Region | 19p13.11 |
| Chromosome id | chr19 |
| Chromosome position | 19678719 |
| Reported gene | ZNF101 |
| Mapped gene | ZNF101 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 94039 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2304130-A |
| SNPs | rs2304130 |
| Merged | 0 |
| SNP id current | 2304130 |
| Context | splice_region_variant |
| Intergenic | 0 |
| Allele frequency | 0.906 |
| P value | 0.0000005 |
| Pvalue mlog | 6.30102999566398 |
| P value text | |
| Or beta | 0.028 |
| %95 Ci | [0.017-0.038] kg/m2 increase |
| Platform | Affymetrix, Illumina [2550021] |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST002783 |
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