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SNP Detail For rs715
1.Mapping Information
| Human SNP ID | rs715 |
|---|---|
| Human chromosome | chr2 |
| Human SNP position | 210678331 |
| Pig chromosome | chr15 |
| Pig SNP position | 125278450 |
2.Annotation Information
| PubMed ID | 23378610 |
|---|---|
| Journal | Diabetes |
| Link | www.ncbi.nlm.nih.gov/pubmed/23378610 |
| Study | Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes. |
| Disease/Trait | Metabolite levels |
| Initial sample | 1,004 European ancestry individuals |
| Replication sample | 339 European ancestry individuals |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.68 |
| P value | 3E-50 |
| Pvalue mlog | 49.5228787452803 |
| P value text | (glycine) |
| Or beta | 0.61 |
| %95 Ci | [0.53-0.69] unit decrease |
| Platform | Affymetrix [909508] (imputed) |
| CNV | N |
| Mapped trait | insulin sensitivity measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004471 |
| Study accession | GCST001852 |
| PubMed ID | 23969696 |
| Journal | Circulation |
| Link | www.ncbi.nlm.nih.gov/pubmed/23969696 |
| Study | Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease. |
| Disease/Trait | Fibrinogen |
| Initial sample | 91,323 European ancestry individuals |
| Replication sample | 8,423 African American individuals, 1,447 Hispanic individuals |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.68 |
| P value | 0.00000000002 |
| Pvalue mlog | 10.698970004336 |
| P value text | (EA) |
| Or beta | 0.009 |
| %95 Ci | [0.007-0.011] unit increase |
| Platform | Affymetrix, Illumina [2515567] (imputed) |
| CNV | N |
| Mapped trait | fibrinogen measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004623 |
| Study accession | GCST002147 |
| PubMed ID | 24816252 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24816252 |
| Study | An atlas of genetic influences on human blood metabolites. |
| Disease/Trait | Blood metabolite levels |
| Initial sample | 7,824 European ancestry individuals |
| Replication sample | NA |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.71 |
| P value | 2E-147 |
| Pvalue mlog | 146.698970004336 |
| P value text | (glycine) |
| Or beta | 0.076 |
| %95 Ci | [0.07-0.082] unit decrease |
| Platform | Affymetrix, Illumina [2100000] (imputed) |
| CNV | N |
| Mapped trait | blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002443 |
| PubMed ID | 24816252 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24816252 |
| Study | An atlas of genetic influences on human blood metabolites. |
| Disease/Trait | Blood metabolite levels |
| Initial sample | 7,824 European ancestry individuals |
| Replication sample | NA |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.71 |
| P value | 7E-58 |
| Pvalue mlog | 57.1549019599857 |
| P value text | (N-acetylglycine) |
| Or beta | 0.091 |
| %95 Ci | [0.079-0.103] unit decrease |
| Platform | Affymetrix, Illumina [2100000] (imputed) |
| CNV | N |
| Mapped trait | blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002443 |
| PubMed ID | 24816252 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24816252 |
| Study | An atlas of genetic influences on human blood metabolites. |
| Disease/Trait | Blood metabolite levels |
| Initial sample | 7,824 European ancestry individuals |
| Replication sample | NA |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.72 |
| P value | 7E-35 |
| Pvalue mlog | 34.1549019599857 |
| P value text | (X-08988) |
| Or beta | 0.033 |
| %95 Ci | [0.027-0.039] unit decrease |
| Platform | Affymetrix, Illumina [2100000] (imputed) |
| CNV | N |
| Mapped trait | blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002443 |
| PubMed ID | 24816252 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24816252 |
| Study | An atlas of genetic influences on human blood metabolites. |
| Disease/Trait | Blood metabolite levels |
| Initial sample | 7,824 European ancestry individuals |
| Replication sample | NA |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.71 |
| P value | 1E-24 |
| Pvalue mlog | 24 |
| P value text | (creatine) |
| Or beta | 0.045 |
| %95 Ci | [0.037-0.053] unit decrease |
| Platform | Affymetrix, Illumina [2100000] (imputed) |
| CNV | N |
| Mapped trait | blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002443 |
| PubMed ID | 24816252 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24816252 |
| Study | An atlas of genetic influences on human blood metabolites. |
| Disease/Trait | Blood metabolite levels |
| Initial sample | 7,824 European ancestry individuals |
| Replication sample | NA |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.71 |
| P value | 3E-21 |
| Pvalue mlog | 20.5228787452803 |
| P value text | (serine) |
| Or beta | 0.022 |
| %95 Ci | [0.018-0.026] unit decrease |
| Platform | Affymetrix, Illumina [2100000] (imputed) |
| CNV | N |
| Mapped trait | blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002443 |
| PubMed ID | 24816252 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24816252 |
| Study | An atlas of genetic influences on human blood metabolites. |
| Disease/Trait | Blood metabolite levels |
| Initial sample | 7,824 European ancestry individuals |
| Replication sample | NA |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.71 |
| P value | 2E-19 |
| Pvalue mlog | 18.698970004336 |
| P value text | (betaine) |
| Or beta | 0.022 |
| %95 Ci | [0.016-0.028] unit increase |
| Platform | Affymetrix, Illumina [2100000] (imputed) |
| CNV | N |
| Mapped trait | blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002443 |
| PubMed ID | 24816252 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24816252 |
| Study | An atlas of genetic influences on human blood metabolites. |
| Disease/Trait | Blood metabolite levels |
| Initial sample | 7,824 European ancestry individuals |
| Replication sample | NA |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.71 |
| P value | 0.0000000000000002 |
| Pvalue mlog | 15.698970004336 |
| P value text | (pyroglutamine) |
| Or beta | 0.036 |
| %95 Ci | [0.028-0.044] unit increase |
| Platform | Affymetrix, Illumina [2100000] (imputed) |
| CNV | N |
| Mapped trait | blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002443 |
| PubMed ID | 24816252 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24816252 |
| Study | An atlas of genetic influences on human blood metabolites. |
| Disease/Trait | Blood metabolite levels |
| Initial sample | 7,824 European ancestry individuals |
| Replication sample | NA |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.72 |
| P value | 0.0000000000000004 |
| Pvalue mlog | 15.397940008672 |
| P value text | (glutaroyl carnitine) |
| Or beta | 0.022 |
| %95 Ci | [0.016-0.028] unit increase |
| Platform | Affymetrix, Illumina [2100000] (imputed) |
| CNV | N |
| Mapped trait | blood metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005664 |
| Study accession | GCST002443 |
| PubMed ID | 26352407 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26352407 |
| Study | Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality. |
| Disease/Trait | Urinary metabolites |
| Initial sample | 3,861 European ancestry individuals |
| Replication sample | 1,691European ancestry individuals |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-C |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.31 |
| P value | 8E-31 |
| Pvalue mlog | 30.096910013008 |
| P value text | (glycine/threonine) |
| Or beta | 0.1409 |
| %95 Ci | [NR] unit increase |
| Platform | Affymetrix [620456] |
| CNV | N |
| Mapped trait | urinary metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005116 |
| Study accession | GCST003119 |
| PubMed ID | 26352407 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26352407 |
| Study | Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality. |
| Disease/Trait | Urinary metabolites |
| Initial sample | 3,861 European ancestry individuals |
| Replication sample | 1,691European ancestry individuals |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-C |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.31 |
| P value | 3E-25 |
| Pvalue mlog | 24.5228787452803 |
| P value text | (3.555 ppm/2.547 ppm) |
| Or beta | 0.176 |
| %95 Ci | [NR] unit increase |
| Platform | Affymetrix [620456] |
| CNV | N |
| Mapped trait | urinary metabolite measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005116 |
| Study accession | GCST003119 |
| PubMed ID | 26068415 |
| Journal | Nat Commun |
| Link | www.ncbi.nlm.nih.gov/pubmed/26068415 |
| Study | Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. |
| Disease/Trait | Amino acid levels |
| Initial sample | up to 7,478 European ancestry individuals |
| Replication sample | 1,182 European ancestry individuals |
| Region | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1, ACADL |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-T |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.6925 |
| P value | 0.00000000003 |
| Pvalue mlog | 10.5228787452803 |
| P value text | (Serine) |
| Or beta | 0.0311 |
| %95 Ci | [0.022-0.04] unit decrease |
| Platform | Affymetrix, Illumina [at least 296619] (imputed) |
| CNV | N |
| Mapped trait | blood metabolite measurement, amino acid measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005664, http://www.ebi.ac.uk/efo/EFO_0005134 |
| Study accession | GCST002966 |
| 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 | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-C |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.315 |
| P value | 0.000007 |
| Pvalue mlog | 5.15490195998574 |
| P value text | (EA) |
| Or beta | 0.022 |
| %95 Ci | [0.012-0.032] 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 | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-C |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.315 |
| P value | 0.000004 |
| Pvalue mlog | 5.39794000867203 |
| P value text | |
| Or beta | 0.022 |
| %95 Ci | [0.013-0.032] 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 | 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 | 2q34 |
| Chromosome id | chr2 |
| Chromosome position | 210678331 |
| Reported gene | CPS1 |
| Mapped gene | CPS1 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 1373 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs715-C |
| SNPs | rs715 |
| Merged | 0 |
| SNP id current | 715 |
| Context | 3_prime_UTR_variant |
| Intergenic | 0 |
| Allele frequency | 0.32 |
| P value | 0.0000000000000004 |
| Pvalue mlog | 15.397940008672 |
| P value text | |
| Or beta | 0.0082 |
| %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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