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SNP Detail For rs2954029
1.Mapping Information
| Human SNP ID | rs2954029 |
|---|---|
| Human chromosome | chr8 |
| Human SNP position | 125478730 |
| Pig chromosome | chr4 |
| Pig SNP position | 14889269 |
2.Annotation Information
| PubMed ID | 20686565 |
|---|---|
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/20686565 |
| Study | Biological, clinical and population relevance of 95 loci for blood lipids. |
| Disease/Trait | HDL cholesterol |
| Initial sample | 99,900 European ancestry individuals |
| Replication sample | NA |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-T |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.44 |
| P value | 6E-19 |
| Pvalue mlog | 18.2218487496163 |
| P value text | |
| Or beta | 0.61 |
| %95 Ci | [0.47-0.75] mg/dL increase |
| Platform | Affymetrix, Illumina, Perlegen [~ 2600000] (imputed) |
| CNV | N |
| Mapped trait | high density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004612 |
| Study accession | GCST000755 |
| PubMed ID | 20686565 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/20686565 |
| Study | Biological, clinical and population relevance of 95 loci for blood lipids. |
| Disease/Trait | LDL cholesterol |
| Initial sample | 95,454 European ancestry individuals |
| Replication sample | NA |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-A |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.46 |
| P value | 3E-29 |
| Pvalue mlog | 28.5228787452803 |
| P value text | |
| Or beta | 1.84 |
| %95 Ci | [1.51-2.17] mg/dL decrease |
| Platform | Affymetrix, Illumina, Perlegen [~ 2600000] (imputed) |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST000759 |
| PubMed ID | 20686565 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/20686565 |
| Study | Biological, clinical and population relevance of 95 loci for blood lipids. |
| Disease/Trait | Triglycerides |
| Initial sample | 96,598 European ancestry individuals |
| Replication sample | NA |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-T |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.47 |
| P value | 3E-55 |
| Pvalue mlog | 54.5228787452803 |
| P value text | |
| Or beta | 5.64 |
| %95 Ci | [4.88-6.4] mg/dL decrease |
| Platform | Affymetrix, Illumina, Perlegen [~ 2600000] (imputed) |
| CNV | N |
| Mapped trait | triglyceride measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004530 |
| Study accession | GCST000758 |
| PubMed ID | 19060906 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19060906 |
| Study | Common variants at 30 loci contribute to polygenic dyslipidemia. |
| Disease/Trait | Triglycerides |
| Initial sample | 19,840 European ancestry individuals |
| Replication sample | Up to 20,623 European ancestry individuals |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-T |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.44 |
| P value | 3E-19 |
| Pvalue mlog | 18.5228787452803 |
| P value text | |
| Or beta | 0.11 |
| %95 Ci | [0.07-0.15] s.d. decrease |
| Platform | Affymetrix, Illumina [~ 2600000] (imputed) |
| CNV | N |
| Mapped trait | triglyceride measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004530 |
| Study accession | GCST000286 |
| 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 | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-T |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.46 |
| P value | 0.00000000002 |
| Pvalue mlog | 10.698970004336 |
| P value text | |
| Or beta | 0.04 |
| %95 Ci | [0.03-0.05] 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 | 20686565 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/20686565 |
| Study | Biological, clinical and population relevance of 95 loci for blood lipids. |
| Disease/Trait | Cholesterol, total |
| Initial sample | 100,184 European ancestry individuals |
| Replication sample | NA |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-A |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.46 |
| P value | 5E-36 |
| Pvalue mlog | 35.3010299956639 |
| P value text | |
| Or beta | 2.3 |
| %95 Ci | [1.93-2.67] mg/dL decrease |
| Platform | Affymetrix, Illumina, Perlegen [~ 2600000] (imputed) |
| CNV | N |
| Mapped trait | total cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004574 |
| Study accession | GCST000760 |
| PubMed ID | 20139978 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20139978 |
| Study | Genome-wide association study of hematological and biochemical traits in a Japanese population. |
| Disease/Trait | Triglycerides |
| Initial sample | 8,993 Japanese ancestry individuals |
| Replication sample | NA |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-T |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.53 |
| P value | 0.0000003 |
| Pvalue mlog | 6.52287874528033 |
| P value text | |
| Or beta | 0.076 |
| %95 Ci | [0.047-0.105] unit decrease |
| Platform | Illumina [561583] |
| CNV | N |
| Mapped trait | triglyceride measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004530 |
| Study accession | GCST000584 |
| PubMed ID | 24097068 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24097068 |
| Study | Discovery and refinement of loci associated with lipid levels. |
| Disease/Trait | HDL cholesterol |
| Initial sample | 94,595 European ancestry individuals |
| Replication sample | 93,982 European ancestry individuals |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-T |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.47 |
| P value | 3E-29 |
| Pvalue mlog | 28.5228787452803 |
| P value text | |
| Or beta | 0.04 |
| %95 Ci | [NR] unit increase |
| Platform | NR [NR] (imputed) |
| CNV | N |
| Mapped trait | high density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004612 |
| Study accession | GCST002223 |
| PubMed ID | 24097068 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24097068 |
| Study | Discovery and refinement of loci associated with lipid levels. |
| Disease/Trait | LDL cholesterol |
| Initial sample | 94,595 European ancestry individuals |
| Replication sample | 93,982 European ancestry individuals |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-T |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.47 |
| P value | 2E-50 |
| Pvalue mlog | 49.698970004336 |
| P value text | |
| Or beta | 0.056 |
| %95 Ci | [NR] unit decrease |
| Platform | NR [NR] (imputed) |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST002222 |
| PubMed ID | 24097068 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24097068 |
| Study | Discovery and refinement of loci associated with lipid levels. |
| Disease/Trait | Cholesterol, total |
| Initial sample | 94,595 European ancestry individuals |
| Replication sample | 93,982 European ancestry individuals |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-T |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.47 |
| P value | 2E-65 |
| Pvalue mlog | 64.698970004336 |
| P value text | |
| Or beta | 0.062 |
| %95 Ci | [NR] unit decrease |
| Platform | NR [NR] (imputed) |
| CNV | N |
| Mapped trait | total cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004574 |
| Study accession | GCST002221 |
| PubMed ID | 24097068 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24097068 |
| Study | Discovery and refinement of loci associated with lipid levels. |
| Disease/Trait | Triglycerides |
| Initial sample | 94,595 European ancestry individuals |
| Replication sample | 93,982 European ancestry individuals |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-T |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.47 |
| P value | 1E-107 |
| Pvalue mlog | 107 |
| P value text | |
| Or beta | 0.076 |
| %95 Ci | [NR] mg/dL decrease |
| Platform | NR [NR] (imputed) |
| CNV | N |
| Mapped trait | triglyceride measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004530 |
| Study accession | GCST002216 |
| PubMed ID | 26343387 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26343387 |
| Study | A comprehensive 1000 Genomes-based genome-wide association meta-analysis of coronary artery disease. |
| Disease/Trait | Coronary artery disease |
| Initial sample | 42,096 European ancestry cases, 361 African American cases, 758 Hispanic American cases, 12,658 South Asian ancestry cases, 1,802 Lebanese ancestry cases, 3,614 East Asian ancestry cases, 99,121 European ancestry controls, 2,778 African American controls, |
| Replication sample | NA |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-A |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.551395 |
| P value | 0.000003 |
| Pvalue mlog | 5.52287874528033 |
| P value text | |
| Or beta | 1.04 |
| %95 Ci | [1.03- 1.06] |
| Platform | Affymetrix, Illumina [8600000] (imputed) |
| CNV | N |
| Mapped trait | coronary artery disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000378 |
| Study accession | GCST003116 |
| PubMed ID | 26582766 |
| Journal | Circ Cardiovasc Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26582766 |
| Study | Genetic Susceptibility to Lipid Levels and Lipid Change Over Time and Risk of Incident Hyperlipidemia in Chinese Populations. |
| Disease/Trait | Triglycerides |
| Initial sample | 8,344 Han Chinese ancestry individuals |
| Replication sample | 14,739 Han Chinese ancestry individuals |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-A |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.41 |
| P value | 2E-20 |
| Pvalue mlog | 19.698970004336 |
| P value text | |
| Or beta | 0.023 |
| %95 Ci | [0.019-0.027] unit increase |
| Platform | Affymetrix, Illumina [2573667] (imputed) |
| CNV | N |
| Mapped trait | triglyceride measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004530 |
| Study accession | GCST003217 |
| PubMed ID | 26582766 |
| Journal | Circ Cardiovasc Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26582766 |
| Study | Genetic Susceptibility to Lipid Levels and Lipid Change Over Time and Risk of Incident Hyperlipidemia in Chinese Populations. |
| Disease/Trait | Cholesterol, total |
| Initial sample | 8,344 Han Chinese ancestry individuals |
| Replication sample | 14,739 Han Chinese ancestry individuals |
| Region | 8q24.13 |
| Chromosome id | chr8 |
| Chromosome position | 125478730 |
| Reported gene | TRIB1 |
| Mapped gene | LOC105375745 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 105375745 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs2954029-A |
| SNPs | rs2954029 |
| Merged | 0 |
| SNP id current | 2954029 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.41 |
| P value | 0.00000000001 |
| Pvalue mlog | 11 |
| P value text | |
| Or beta | 2.218 |
| %95 Ci | [1.58-2.85] unit increase |
| Platform | Affymetrix, Illumina [2573667] (imputed) |
| CNV | N |
| Mapped trait | total cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004574 |
| Study accession | GCST003214 |
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and Xi'an University of Technology ©2014-2017 All Rights Reserved.
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