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SNP Detail For rs1800961
1.Mapping Information
| Human SNP ID | rs1800961 |
|---|---|
| Human chromosome | chr20 |
| Human SNP position | 44413724 |
| Pig chromosome | chr17 |
| Pig SNP position | 52280742 |
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 | 20q13.12 |
| Chromosome id | chr20 |
| Chromosome position | 44413724 |
| Reported gene | HNF4A |
| Mapped gene | HNF4A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3172 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1800961-T |
| SNPs | rs1800961 |
| Merged | 0 |
| SNP id current | 1800961 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.03 |
| P value | 0.000000000000001 |
| Pvalue mlog | 15 |
| P value text | |
| Or beta | 1.88 |
| %95 Ci | [1.41-2.35] mg/dL decrease |
| 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 | 19060906 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19060906 |
| Study | Common variants at 30 loci contribute to polygenic dyslipidemia. |
| Disease/Trait | HDL cholesterol |
| Initial sample | 19,840 European ancestry individuals |
| Replication sample | Up to 20,623 European ancestry individuals |
| Region | 20q13.12 |
| Chromosome id | chr20 |
| Chromosome position | 44413724 |
| Reported gene | HNF4A |
| Mapped gene | HNF4A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3172 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1800961-T |
| SNPs | rs1800961 |
| Merged | 0 |
| SNP id current | 1800961 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.03 |
| P value | 0.0000000008 |
| Pvalue mlog | 9.09691001300805 |
| P value text | |
| Or beta | 0.19 |
| %95 Ci | [0.09-0.29] s.d. decrease |
| Platform | Affymetrix, Illumina [~ 2600000] (imputed) |
| CNV | N |
| Mapped trait | high density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004612 |
| Study accession | GCST000290 |
| PubMed ID | 21300955 |
| Journal | Circulation |
| Link | www.ncbi.nlm.nih.gov/pubmed/21300955 |
| Study | Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels. |
| Disease/Trait | C-reactive protein levels |
| Initial sample | 63,678 European ancestry individuals 1,792 Erasmus Ruchpen individuals, 715 Orcadian individuals |
| Replication sample | 16,540 European ancestry individuals |
| Region | 20q13.12 |
| Chromosome id | chr20 |
| Chromosome position | 44413724 |
| Reported gene | HNF4A |
| Mapped gene | HNF4A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3172 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1800961-C |
| SNPs | rs1800961 |
| Merged | 0 |
| SNP id current | 1800961 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000002 |
| Pvalue mlog | 8.69897000433601 |
| P value text | |
| Or beta | 0.088 |
| %95 Ci | [0.06-0.12] unit increase |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | C-reactive protein measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004458 |
| Study accession | GCST000965 |
| 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 | 20q13.12 |
| Chromosome id | chr20 |
| Chromosome position | 44413724 |
| Reported gene | HNF4A |
| Mapped gene | HNF4A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3172 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1800961-T |
| SNPs | rs1800961 |
| Merged | 0 |
| SNP id current | 1800961 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.03 |
| P value | 0.0000000000006 |
| Pvalue mlog | 12.2218487496163 |
| P value text | |
| Or beta | 4.73 |
| %95 Ci | [3.44-6.02] 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 | 22939635 |
| Journal | Am J Hum Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/22939635 |
| Study | Genome-wide association and population genetic analysis of C-reactive protein in African American and Hispanic American women. |
| Disease/Trait | C-reactive protein |
| Initial sample | 8,280 African American female individuals, 3,548 Hispanic female individuals |
| Replication sample | 3,787 African American female individuals, 3,548 Hispanic female individuals, 5,656 European ancestry individuals |
| Region | 20q13.12 |
| Chromosome id | chr20 |
| Chromosome position | 44413724 |
| Reported gene | HNF4A |
| Mapped gene | HNF4A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3172 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1800961-T |
| SNPs | rs1800961 |
| Merged | 0 |
| SNP id current | 1800961 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.04 |
| P value | 0.000008 |
| Pvalue mlog | 5.09691001300805 |
| P value text | (HA women) |
| Or beta | 0.268 |
| %95 Ci | [0.15-0.39] unit decrease |
| Platform | Affymetrix [up to 2203609] (imputed) |
| CNV | N |
| Mapped trait | C-reactive protein measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004458 |
| Study accession | GCST001650 |
| 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 | 20q13.12 |
| Chromosome id | chr20 |
| Chromosome position | 44413724 |
| Reported gene | HNF4A |
| Mapped gene | HNF4A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3172 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1800961-T |
| SNPs | rs1800961 |
| Merged | 0 |
| SNP id current | 1800961 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.05 |
| P value | 2E-34 |
| Pvalue mlog | 33.698970004336 |
| P value text | |
| Or beta | 0.127 |
| %95 Ci | [NR] unit decrease |
| 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 | Cholesterol, total |
| Initial sample | 94,595 European ancestry individuals |
| Replication sample | 93,982 European ancestry individuals |
| Region | 20q13.12 |
| Chromosome id | chr20 |
| Chromosome position | 44413724 |
| Reported gene | HNF4A |
| Mapped gene | HNF4A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3172 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1800961-T |
| SNPs | rs1800961 |
| Merged | 0 |
| SNP id current | 1800961 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.05 |
| P value | 1E-24 |
| Pvalue mlog | 24 |
| P value text | |
| Or beta | 0.106 |
| %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 | 25961943 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/25961943 |
| Study | The impact of low-frequency and rare variants on lipid levels. |
| Disease/Trait | HDL cholesterol |
| Initial sample | up to 62,166 European ancestry individuals |
| Replication sample | NA |
| Region | 20q13.12 |
| Chromosome id | chr20 |
| Chromosome position | 44413724 |
| Reported gene | HNF4A |
| Mapped gene | HNF4A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3172 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1800961-C |
| SNPs | rs1800961 |
| Merged | 0 |
| SNP id current | 1800961 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.96 |
| P value | 5E-20 |
| Pvalue mlog | 19.3010299956639 |
| P value text | |
| Or beta | 0.149 |
| %95 Ci | [0.12-0.18] s.d. increase |
| Platform | Affymetrix, Illumina, Perlegen [up to 9657952] (imputed) |
| CNV | N |
| Mapped trait | high density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004612 |
| Study accession | GCST002899 |
| PubMed ID | 26561523 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26561523 |
| Study | A meta-analysis of 120,246 individuals identifies 18 new loci for fibrinogen concentration. |
| Disease/Trait | Fibrinogen levels |
| Initial sample | 120,246 European ancestry individuals |
| Replication sample | NA |
| Region | 20q13.12 |
| Chromosome id | chr20 |
| Chromosome position | 44413724 |
| Reported gene | HNF4A |
| Mapped gene | HNF4A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 3172 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1800961-T |
| SNPs | rs1800961 |
| Merged | 0 |
| SNP id current | 1800961 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.03 |
| P value | 0.0000000001 |
| Pvalue mlog | 10 |
| P value text | |
| Or beta | 0.017 |
| %95 Ci | NR unit decrease |
| Platform | Affymetrix, Illumina [~ 10700000] (imputed) |
| CNV | N |
| Mapped trait | fibrinogen measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004623 |
| Study accession | GCST003194 |
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