PigVar
Overview
Pig SNPs
SNP Table
SNP Hit on Gene
SNP Coding
SNP lincRNA
Search SNPs by Region
Browse on Chromosome
SV
Positive Selection
Help
Manual
Pipeline
Data Statistics
Contact Us
Download
SNP Detail For rs6882076
1.Mapping Information
| Human SNP ID | rs6882076 |
|---|---|
| Human chromosome | chr5 |
| Human SNP position | 156963286 |
| Pig chromosome | chr16 |
| Pig SNP position | 72143524 |
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 | LDL cholesterol |
| Initial sample | 95,454 European ancestry individuals |
| Replication sample | NA |
| Region | 5q33.3 |
| Chromosome id | chr5 |
| Chromosome position | 156963286 |
| Reported gene | TIMD4, HAVCR1 |
| Mapped gene | TIMD4 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 91937 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6882076-T |
| SNPs | rs6882076 |
| Merged | 0 |
| SNP id current | 6882076 |
| Context | upstream_gene_variant |
| Intergenic | 0 |
| Allele frequency | 0.35 |
| P value | 2E-22 |
| Pvalue mlog | 21.698970004336 |
| P value text | |
| Or beta | 1.67 |
| %95 Ci | [1.3-2.04] 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 | 5q33.3 |
| Chromosome id | chr5 |
| Chromosome position | 156963286 |
| Reported gene | TIMD4, HAVCR1 |
| Mapped gene | TIMD4 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 91937 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6882076-G |
| SNPs | rs6882076 |
| Merged | 0 |
| SNP id current | 6882076 |
| Context | upstream_gene_variant |
| Intergenic | 0 |
| Allele frequency | 0.36 |
| P value | 0.000000000004 |
| Pvalue mlog | 11.397940008672 |
| P value text | |
| Or beta | 2.63 |
| %95 Ci | [1.87-3.39] 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 | 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 | 5q33.3 |
| Chromosome id | chr5 |
| Chromosome position | 156963286 |
| Reported gene | TIMD4, HAVCR1 |
| Mapped gene | TIMD4 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 91937 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6882076-T |
| SNPs | rs6882076 |
| Merged | 0 |
| SNP id current | 6882076 |
| Context | upstream_gene_variant |
| Intergenic | 0 |
| Allele frequency | 0.35 |
| P value | 7E-28 |
| Pvalue mlog | 27.1549019599857 |
| P value text | |
| Or beta | 1.98 |
| %95 Ci | [1.59-2.37] 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 | 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 | 5q33.3 |
| Chromosome id | chr5 |
| Chromosome position | 156963286 |
| Reported gene | TIMD4 |
| Mapped gene | TIMD4 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 91937 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6882076-T |
| SNPs | rs6882076 |
| Merged | 0 |
| SNP id current | 6882076 |
| Context | upstream_gene_variant |
| Intergenic | 0 |
| Allele frequency | 0.36 |
| P value | 3E-31 |
| Pvalue mlog | 30.5228787452803 |
| P value text | |
| Or beta | 0.046 |
| %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 | 5q33.3 |
| Chromosome id | chr5 |
| Chromosome position | 156963286 |
| Reported gene | TIMD4 |
| Mapped gene | TIMD4 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 91937 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6882076-T |
| SNPs | rs6882076 |
| Merged | 0 |
| SNP id current | 6882076 |
| Context | upstream_gene_variant |
| Intergenic | 0 |
| Allele frequency | 0.36 |
| P value | 5E-41 |
| Pvalue mlog | 40.3010299956639 |
| P value text | |
| Or beta | 0.051 |
| %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 | 5q33.3 |
| Chromosome id | chr5 |
| Chromosome position | 156963286 |
| Reported gene | TIMD4 |
| Mapped gene | TIMD4 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 91937 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs6882076-T |
| SNPs | rs6882076 |
| Merged | 0 |
| SNP id current | 6882076 |
| Context | upstream_gene_variant |
| Intergenic | 0 |
| Allele frequency | 0.36 |
| P value | 0.000000000000002 |
| Pvalue mlog | 14.698970004336 |
| P value text | |
| Or beta | 0.029 |
| %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 |
|
Kunming Institute of Zoology, CAS
and Xi'an University of Technology ©2014-2017 All Rights Reserved.
|
|