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SNP Detail For rs780093
1.Mapping Information
| Human SNP ID | rs780093 |
|---|---|
| Human chromosome | chr2 |
| Human SNP position | 27519736 |
| Pig chromosome | chr3 |
| Pig SNP position | 118819925 |
2.Annotation Information
| PubMed ID | 20705733 |
|---|---|
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20705733 |
| Study | Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels. |
| Disease/Trait | Calcium levels |
| Initial sample | 20,611 European ancestry individuals |
| Replication sample | NA |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | FNDC4, IFT172, GCKR, C2orf16 |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-T |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000007 |
| Pvalue mlog | 5.15490195998574 |
| P value text | |
| Or beta | 0.02 |
| %95 Ci | [NR] unit increase |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | calcium measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004838 |
| Study accession | GCST000769 |
| PubMed ID | 20884846 |
| Journal | Circ Cardiovasc Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20884846 |
| Study | Multiple genetic loci influence serum urate levels and their relationship with gout and cardiovascular disease risk factors. |
| Disease/Trait | Urate levels |
| Initial sample | 28,283 European ancestry individuals |
| Replication sample | 22,054 European ancestry individuals |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | GCKR |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-T |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.4 |
| P value | 0.00000000000000004 |
| Pvalue mlog | 16.397940008672 |
| P value text | (Urate) |
| Or beta | 5.15 |
| %95 Ci | [3.95-6.35] umol/l increase |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | urate measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004531 |
| Study accession | GCST000818 |
| PubMed ID | 21386085 |
| Journal | Diabetes |
| Link | www.ncbi.nlm.nih.gov/pubmed/21386085 |
| Study | A bivariate genome-wide approach to metabolic syndrome: STAMPEED consortium. |
| Disease/Trait | Triglycerides-Blood Pressure (TG-BP) |
| Initial sample | 22,161 European ancestry individuals |
| Replication sample | NA |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | GCKR |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-A |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.0000000003 |
| Pvalue mlog | 9.52287874528033 |
| P value text | |
| Or beta | 0.18 |
| %95 Ci | [0.12-0.24] unit increase |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | triglyceride measurement, blood pressure |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004530, http://www.ebi.ac.uk/efo/EFO_0004325 |
| Study accession | GCST001004 |
| PubMed ID | 21386085 |
| Journal | Diabetes |
| Link | www.ncbi.nlm.nih.gov/pubmed/21386085 |
| Study | A bivariate genome-wide approach to metabolic syndrome: STAMPEED consortium. |
| Disease/Trait | Waist Circumference - Triglycerides (WC-TG) |
| Initial sample | 22,161 European ancestry individuals |
| Replication sample | NA |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | GCKR |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-A |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000000000002 |
| Pvalue mlog | 11.698970004336 |
| P value text | |
| Or beta | 0.19 |
| %95 Ci | [0.13-0.25] unit increase |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | triglyceride measurement, metabolic syndrome |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004530, http://www.ebi.ac.uk/efo/EFO_0000195 |
| Study accession | GCST001006 |
| PubMed ID | 22747683 |
| Journal | BMC Med Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/22747683 |
| Study | Genetic variants associated with breast size also influence breast cancer risk. |
| Disease/Trait | Breast size |
| Initial sample | 16,175 European ancestry female individuals |
| Replication sample | NA |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | SLC4A1AP |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-T |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.416 |
| P value | 0.000005 |
| Pvalue mlog | 5.30102999566398 |
| P value text | |
| Or beta | 0.072 |
| %95 Ci | [0.041-0.103] cup size increase |
| Platform | Illumina [7422970] (imputed) |
| CNV | N |
| Mapped trait | breast size, breast carcinoma |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004884, http://www.ebi.ac.uk/efo/EFO_0000305 |
| Study accession | GCST001585 |
| PubMed ID | 22829776 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/22829776 |
| Study | A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation. |
| Disease/Trait | Sex hormone-binding globulin levels |
| Initial sample | 21,791 European ancestry individuals |
| Replication sample | 8,175 European ancestry individuals |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | GCKR |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-T |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.4 |
| P value | 0.0000000000000002 |
| Pvalue mlog | 15.698970004336 |
| P value text | (Men + Women) |
| Or beta | 0.032 |
| %95 Ci | [0.024-0.040] nmol/L decrease |
| Platform | Affymetrix, Illumina [2543887] (imputed) |
| CNV | N |
| Mapped trait | sex hormone globulin binding measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004696 |
| Study accession | GCST001612 |
| PubMed ID | 22829776 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/22829776 |
| Study | A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation. |
| Disease/Trait | Sex hormone-binding globulin levels |
| Initial sample | 21,791 European ancestry individuals |
| Replication sample | 8,175 European ancestry individuals |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | GCKR |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-T |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.4 |
| P value | 0.00000007 |
| Pvalue mlog | 7.15490195998574 |
| P value text | (Men) |
| Or beta | 0.026 |
| %95 Ci | [0.016-0.036] nmol/L decrease |
| Platform | Affymetrix, Illumina [2543887] (imputed) |
| CNV | N |
| Mapped trait | sex hormone globulin binding measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004696 |
| Study accession | GCST001612 |
| PubMed ID | 22829776 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/22829776 |
| Study | A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation. |
| Disease/Trait | Sex hormone-binding globulin levels |
| Initial sample | 21,791 European ancestry individuals |
| Replication sample | 8,175 European ancestry individuals |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | GCKR |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-T |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.4 |
| P value | 0.00000000009 |
| Pvalue mlog | 10.0457574905606 |
| P value text | (Women) |
| Or beta | 0.041 |
| %95 Ci | [0.029-0.053] nmol/L decrease |
| Platform | Affymetrix, Illumina [2543887] (imputed) |
| CNV | N |
| Mapped trait | sex hormone globulin binding measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004696 |
| Study accession | GCST001612 |
| PubMed ID | 21102463 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21102463 |
| Study | Genome-wide meta-analysis increases to 71 the number of confirmed Crohn__s disease susceptibility loci. |
| Disease/Trait | Crohn__s disease |
| Initial sample | 6,333 European ancestry cases, 15,056 European ancestry controls |
| Replication sample | 15,694 European ancestry cases, 14,026 European ancestry controls, 414 European ancestry trios |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | GCKR |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-T |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.418 |
| P value | 0.00000000005 |
| Pvalue mlog | 10.3010299956639 |
| P value text | |
| Or beta | 1.15 |
| %95 Ci | [1.10-1.21] |
| Platform | Affymetrix, Illumina [953241] (imputed) |
| CNV | N |
| Mapped trait | Crohn__s disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000384 |
| Study accession | GCST000879 |
| PubMed ID | 23362303 |
| Journal | Circ Cardiovasc Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23362303 |
| Study | Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu |
| Disease/Trait | Palmitic acid (16:0) plasma levels |
| Initial sample | 8,961 European ancestry individuals |
| Replication sample | |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | GCKR |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-T |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 0.000003 |
| Pvalue mlog | 5.52287874528033 |
| P value text | |
| Or beta | 0.1261 |
| %95 Ci | unit increase |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | phospholipid measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004639 |
| Study accession | GCST001838 |
| PubMed ID | 23362303 |
| Journal | Circ Cardiovasc Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23362303 |
| Study | Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu |
| Disease/Trait | Palmitoleic acid (16:1n-7) plasma levels |
| Initial sample | 8,961 European ancestry individuals |
| Replication sample | |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | ZNF512, XAB1, GCKR, C2orf16 |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-T |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.41 |
| P value | 0.000000001 |
| Pvalue mlog | 9 |
| P value text | |
| Or beta | 0.02 |
| %95 Ci | [0.014-0.027] unit increase |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | phospholipid measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004639 |
| Study accession | GCST001841 |
| PubMed ID | 25524916 |
| Journal | Diabetes |
| Link | www.ncbi.nlm.nih.gov/pubmed/25524916 |
| Study | Genetic Variants Associated with Quantitative Glucose Homeostasis Traits Translate to Type 2 Diabetes in Mexican Americans: The GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium. |
| Disease/Trait | Glucose homeostasis traits |
| Initial sample | up to 4,176 Mexican American individuals |
| Replication sample | NA |
| Region | 2p23.3 |
| Chromosome id | chr2 |
| Chromosome position | 27519736 |
| Reported gene | GCKR |
| Mapped gene | GCKR |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2646 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs780093-? |
| SNPs | rs780093 |
| Merged | 0 |
| SNP id current | 780093 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | |
| P value | 0.000001 |
| Pvalue mlog | 6 |
| P value text | (SG) |
| Or beta | 0.14 |
| %95 Ci | [0.081-0.199] unit increase |
| Platform | Illumina [693128] |
| CNV | N |
| Mapped trait | glucose homeostasis measurement, glucose effectiveness measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0006896, http://www.ebi.ac.uk/efo/EFO_0006833 |
| Study accession | GCST002726 |
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and Xi'an University of Technology ©2014-2017 All Rights Reserved.
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