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SNP Detail For rs599839
1.Mapping Information
| Human SNP ID | rs599839 |
|---|---|
| Human chromosome | chr1 |
| Human SNP position | 109279544 |
| Pig chromosome | chr4 |
| Pig SNP position | 121297731 |
2.Annotation Information
| PubMed ID | 18262040 |
|---|---|
| Journal | Lancet |
| Link | www.ncbi.nlm.nih.gov/pubmed/18262040 |
| Study | LDL-cholesterol concentrations: a genome-wide association study. |
| Disease/Trait | LDL cholesterol |
| Initial sample | 11,685 European ancestry individuals |
| Replication sample | Up to 4,979 European ancestry individuals |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109279544 |
| Reported gene | CELSR2, PSRC1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 3788 |
| Downstream gene distance | 10 |
| SNP risk allele | rs599839-G |
| SNPs | rs599839 |
| Merged | 0 |
| SNP id current | 599839 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.19 |
| P value | 1E-33 |
| Pvalue mlog | 33 |
| P value text | |
| Or beta | 0.16 |
| %95 Ci | [0.14-0.18] mmol/L decrease |
| Platform | Affymetrix, Illumina [up to 461986] |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST000151 |
| PubMed ID | 18193043 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/18193043 |
| Study | Newly identified loci that influence lipid concentrations and risk of coronary artery disease. |
| Disease/Trait | LDL cholesterol |
| Initial sample | 8,589 European ancestry individuals |
| Replication sample | 12,981 European ancestry individuals |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109279544 |
| Reported gene | CELSR2, PSRC1, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 3788 |
| Downstream gene distance | 10 |
| SNP risk allele | rs599839-A |
| SNPs | rs599839 |
| Merged | 0 |
| SNP id current | 599839 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.77 |
| P value | 6E-33 |
| Pvalue mlog | 32.2218487496163 |
| P value text | |
| Or beta | 5.48 |
| %95 Ci | [NR] mg/dl increase |
| Platform | Affymetrix, Illumina [~ 2261000] (imputed) |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST000132 |
| PubMed ID | 18179892 |
| Journal | Am J Hum Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/18179892 |
| Study | Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia. |
| Disease/Trait | LDL cholesterol |
| Initial sample | 1,955 European ancestry hypertensive individuals |
| Replication sample | 2,033 European ancestry individuals from 519 families, 1,461 European ancestry twins |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109279544 |
| Reported gene | PSRC1, CELSR2 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 3788 |
| Downstream gene distance | 10 |
| SNP risk allele | rs599839-G |
| SNPs | rs599839 |
| Merged | 0 |
| SNP id current | 599839 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.24 |
| P value | 0.0000001 |
| Pvalue mlog | 7 |
| P value text | |
| Or beta | 0.95 |
| %95 Ci | [0.93-0.97] mMol/l increase |
| Platform | Affymetrix [400496] |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST000131 |
| PubMed ID | 17634449 |
| Journal | N Engl J Med |
| Link | www.ncbi.nlm.nih.gov/pubmed/17634449 |
| Study | Genomewide association analysis of coronary artery disease. |
| Disease/Trait | Coronary heart disease |
| Initial sample | 1,926 European ancestry cases, 2,938 European ancestry controls |
| Replication sample | 875 European ancestry cases, 1,644 European ancestry controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109279544 |
| Reported gene | PSRC1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 3788 |
| Downstream gene distance | 10 |
| SNP risk allele | rs599839-A |
| SNPs | rs599839 |
| Merged | 0 |
| SNP id current | 599839 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.77 |
| P value | 0.000000004 |
| Pvalue mlog | 8.39794000867203 |
| P value text | |
| Or beta | 1.29 |
| %95 Ci | [1.18-1.40] |
| Platform | Affymetrix [377857] |
| CNV | N |
| Mapped trait | coronary heart disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001645 |
| Study accession | GCST000057 |
| PubMed ID | 21909109 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21909109 |
| Study | Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits. |
| Disease/Trait | Metabolite levels |
| Initial sample | 12,545 Korean ancestry individuals |
| Replication sample | Up to 30,395 East Asian ancestry individuals |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109279544 |
| Reported gene | CELSR2, PSRC1, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 3788 |
| Downstream gene distance | 10 |
| SNP risk allele | rs599839-G |
| SNPs | rs599839 |
| Merged | 0 |
| SNP id current | 599839 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.06 |
| P value | 2E-19 |
| Pvalue mlog | 18.698970004336 |
| P value text | (LDL) |
| Or beta | 5.2254 |
| %95 Ci | [4.09-6.37] mg/dL decrease |
| Platform | Affymetrix [~ 2200000] (imputed) |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST001233 |
| PubMed ID | 21378990 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21378990 |
| Study | Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. |
| Disease/Trait | Coronary heart disease |
| Initial sample | 22,233 European ancestry cases, 64,762 European ancestry controls |
| Replication sample | 56,682 European ancestry cases and controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109279544 |
| Reported gene | SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 3788 |
| Downstream gene distance | 10 |
| SNP risk allele | rs599839-A |
| SNPs | rs599839 |
| Merged | 0 |
| SNP id current | 599839 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.78 |
| P value | 0.0000000003 |
| Pvalue mlog | 9.52287874528033 |
| P value text | |
| Or beta | 1.11 |
| %95 Ci | [1.08-1.15] |
| Platform | Affymetrix, Illumina [~ 2300000] (imputed) |
| CNV | N |
| Mapped trait | coronary heart disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001645 |
| Study accession | GCST000998 |
| PubMed ID | 20442857 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20442857 |
| Study | Genome-wide association study of Lp-PLA(2) activity and mass in the Framingham Heart Study. |
| Disease/Trait | Lipoprotein-associated phospholipase A2 activity and mass |
| Initial sample | 6,668 European ancestry individuals |
| Replication sample | NA |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109279544 |
| Reported gene | PSRC1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 3788 |
| Downstream gene distance | 10 |
| SNP risk allele | rs599839-G |
| SNPs | rs599839 |
| Merged | 0 |
| SNP id current | 599839 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.22 |
| P value | 0.000000000000003 |
| Pvalue mlog | 14.5228787452803 |
| P value text | (activity) |
| Or beta | 5.5 |
| %95 Ci | [NR] nmol/ml/min decrease |
| Platform | Affymetrix [360811] |
| CNV | N |
| Mapped trait | lipoprotein-associated phospholipase A(2) measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004746 |
| Study accession | GCST000671 |
| PubMed ID | 24262325 |
| Journal | Stroke |
| Link | www.ncbi.nlm.nih.gov/pubmed/24262325 |
| Study | Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. |
| Disease/Trait | Coronary artery disease or ischemic stroke |
| Initial sample | 12,389 Ischemic stroke cases, 22,233 Coronary artery disease cases, ~ 88,766 controls |
| Replication sample | NA |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109279544 |
| Reported gene | SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 3788 |
| Downstream gene distance | 10 |
| SNP risk allele | rs599839-? |
| SNPs | rs599839 |
| Merged | 0 |
| SNP id current | 599839 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | |
| P value | 0.00000001 |
| Pvalue mlog | 8 |
| P value text | |
| Or beta | |
| %95 Ci | |
| Platform | Affymetrix, Illumina [up to 2500000] (imputed) |
| CNV | N |
| Mapped trait | stroke, coronary heart disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000712, http://www.ebi.ac.uk/efo/EFO_0001645 |
| Study accession | GCST002287 |
| PubMed ID | 24262325 |
| Journal | Stroke |
| Link | www.ncbi.nlm.nih.gov/pubmed/24262325 |
| Study | Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. |
| Disease/Trait | Coronary artery disease or large artery stroke |
| Initial sample | 2,167 Large artery stroke cases, 22,233 Coronary artery disease cases, ~ 75,921 controls |
| Replication sample | NA |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109279544 |
| Reported gene | SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 3788 |
| Downstream gene distance | 10 |
| SNP risk allele | rs599839-? |
| SNPs | rs599839 |
| Merged | 0 |
| SNP id current | 599839 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | |
| P value | 0.00000000000000008 |
| Pvalue mlog | 16.096910013008 |
| P value text | |
| Or beta | |
| %95 Ci | |
| Platform | Affymetrix, Illumina [up to 2500000] (imputed) |
| CNV | N |
| Mapped trait | large artery stroke, coronary heart disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005524, http://www.ebi.ac.uk/efo/EFO_0001645 |
| Study accession | GCST002290 |
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and Xi'an University of Technology ©2014-2017 All Rights Reserved.
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