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SNP Detail For rs13107325
1.Mapping Information
| Human SNP ID | rs13107325 |
|---|---|
| Human chromosome | chr4 |
| Human SNP position | 102267552 |
| Pig chromosome | chr8 |
| Pig SNP position | 127757384 |
2.Annotation Information
| PubMed ID | 21909110 |
|---|---|
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21909110 |
| Study | Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure. |
| Disease/Trait | Blood pressure |
| Initial sample | 74,064 European ancestry individuals |
| Replication sample | 48,607 European ancestry individuals |
| Region | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.12 |
| P value | 0.0000000001 |
| Pvalue mlog | 10 |
| P value text | (Mean Arterial Pressure) |
| Or beta | 0.633 |
| %95 Ci | [0.44-0.82] mmHg decrease |
| Platform | Affymetrix, Illumina, Perlegen [NR] (imputed) |
| CNV | N |
| Mapped trait | mean arterial pressure |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0006340 |
| Study accession | GCST001236 |
| PubMed ID | 21909115 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/21909115 |
| Study | Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. |
| Disease/Trait | Diastolic blood pressure |
| Initial sample | 69,395 European ancestry individuals |
| Replication sample | Up to 133,361 European ancestry individuals |
| Region | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.05 |
| P value | 0.00000000000000002 |
| Pvalue mlog | 16.698970004336 |
| P value text | |
| Or beta | 0.684 |
| %95 Ci | [NR] mmHg decrease |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | diastolic blood pressure |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0006336 |
| Study accession | GCST001228 |
| PubMed ID | 21909115 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/21909115 |
| Study | Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. |
| Disease/Trait | Systolic blood pressure |
| Initial sample | 69,395 European ancestry individuals |
| Replication sample | Up to 133,361 European ancestry individuals |
| Region | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.05 |
| P value | 0.00000000000003 |
| Pvalue mlog | 13.5228787452803 |
| P value text | |
| Or beta | 0.981 |
| %95 Ci | [NR] mmHg decrease |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | systolic blood pressure |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0006335 |
| Study accession | GCST001227 |
| PubMed ID | 21909115 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/21909115 |
| Study | Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. |
| Disease/Trait | Hypertension |
| Initial sample | 69,395 European ancestry individuals |
| Replication sample | Up to 133,361 European ancestry individuals |
| Region | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.05 |
| P value | 0.0000005 |
| Pvalue mlog | 6.30102999566398 |
| P value text | |
| Or beta | 0.105 |
| %95 Ci | [NR] unit decrease |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | hypertension |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000537 |
| Study accession | GCST001238 |
| 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 | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.07 |
| P value | 0.00000000007 |
| Pvalue mlog | 10.1549019599857 |
| P value text | |
| Or beta | 0.84 |
| %95 Ci | [0.53-1.15] 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 | 20935630 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20935630 |
| Study | Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. |
| Disease/Trait | Body mass index |
| Initial sample | Up to 123,865 European ancestry individuals |
| Replication sample | Up to 125,931 European ancestry individuals |
| Region | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.07 |
| P value | 0.0000000000002 |
| Pvalue mlog | 12.698970004336 |
| P value text | |
| Or beta | 0.19 |
| %95 Ci | [0.11-0.27] kg/m2 increase |
| Platform | Affymetrix, Illumina, Perlegen [~ 2800000] (imputed) |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST000830 |
| 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 | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.08 |
| P value | 0.000000000000001 |
| Pvalue mlog | 15 |
| P value text | |
| Or beta | 0.071 |
| %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 | 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 | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.074 |
| P value | 0.000000003 |
| Pvalue mlog | 8.52287874528033 |
| P value text | (EA, men) |
| Or beta | 0.053 |
| %95 Ci | [0.035-0.07] 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 | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.071 |
| P value | 0.0000003 |
| Pvalue mlog | 6.52287874528033 |
| P value text | (EA, women) |
| Or beta | 0.045 |
| %95 Ci | [0.028-0.062] 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 | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.072 |
| P value | 0.000000000002 |
| Pvalue mlog | 11.698970004336 |
| P value text | (EA) |
| Or beta | 0.048 |
| %95 Ci | [0.034-0.061] 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 | 26198764 |
| Journal | Am J Med Genet B Neuropsychiatr Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26198764 |
| Study | Genome-wide association study of schizophrenia in Ashkenazi Jews. |
| Disease/Trait | Schizophrenia |
| Initial sample | 592 Ashkenazi Jewish ancestry cases, 505 Ashkenazi Jewish ancestry controls, 36,989 cases, 113,075 controls |
| Replication sample | NA |
| Region | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | NR |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000000002 |
| Pvalue mlog | 11.698970004336 |
| P value text | |
| Or beta | 1.16 |
| %95 Ci | [NR] |
| Platform | Illumina [7158791] (imputed) |
| CNV | N |
| Mapped trait | schizophrenia |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000692 |
| Study accession | GCST003048 |
| 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 | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.072 |
| P value | 0.000000000001 |
| Pvalue mlog | 12 |
| P value text | |
| Or beta | 0.047 |
| %95 Ci | [0.034-0.06] 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 | 26604143 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26604143 |
| Study | Genome-wide association analysis identifies three new susceptibility loci for childhood body mass index. |
| Disease/Trait | Childhood body mass index |
| Initial sample | 34,744 European ancestry children |
| Replication sample | 11,313 European ancestry children |
| Region | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | SLC39A8 |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.07 |
| P value | 0.0000004 |
| Pvalue mlog | 6.39794000867203 |
| P value text | |
| Or beta | 0.081 |
| %95 Ci | [0.05-0.112] unit increase |
| Platform | Affymetrix, Illumina [2499691] (imputed) |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST003177 |
| PubMed ID | 26604143 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26604143 |
| Study | Genome-wide association analysis identifies three new susceptibility loci for childhood body mass index. |
| Disease/Trait | Childhood body mass index |
| Initial sample | 34,744 European ancestry children |
| Replication sample | 11,313 European ancestry children |
| Region | 4q24 |
| Chromosome id | chr4 |
| Chromosome position | 102267552 |
| Reported gene | NR |
| Mapped gene | SLC39A8 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 64116 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs13107325-T |
| SNPs | rs13107325 |
| Merged | 0 |
| SNP id current | 13107325 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.00000001 |
| Pvalue mlog | 8 |
| P value text | |
| Or beta | |
| %95 Ci | |
| Platform | Affymetrix, Illumina [2499691] (imputed) |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST003177 |
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