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SNP Detail For rs1354034
1.Mapping Information
| Human SNP ID | rs1354034 |
|---|---|
| Human chromosome | chr3 |
| Human SNP position | 56815721 |
| Pig chromosome | chr13 |
| Pig SNP position | 42687518 |
2.Annotation Information
| PubMed ID | 22139419 |
|---|---|
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/22139419 |
| Study | New gene functions in megakaryopoiesis and platelet formation. |
| Disease/Trait | Mean platelet volume |
| Initial sample | 16,948 European ancestry individuals, 1,652 Val Borbera individuals |
| Replication sample | Up to 18,838 European ancestry individuals |
| Region | 3p14.3 |
| Chromosome id | chr3 |
| Chromosome position | 56815721 |
| Reported gene | ARHGEF3 |
| Mapped gene | ARHGEF3 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 50650 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1354034-T |
| SNPs | rs1354034 |
| Merged | 0 |
| SNP id current | 1354034 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 3E-69 |
| Pvalue mlog | 68.5228787452803 |
| P value text | |
| Or beta | 0.023 |
| %95 Ci | [0.021-0.025] ln(fl) increase |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | mean platelet volume |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004584 |
| Study accession | GCST001335 |
| PubMed ID | 22139419 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/22139419 |
| Study | New gene functions in megakaryopoiesis and platelet formation. |
| Disease/Trait | Platelet count |
| Initial sample | 47,005 European ancestry individuals, 1,661 Val Borbera individuals |
| Replication sample | Up to 18,838 European ancestry individuals |
| Region | 3p14.3 |
| Chromosome id | chr3 |
| Chromosome position | 56815721 |
| Reported gene | ARHGEF3 |
| Mapped gene | ARHGEF3 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 50650 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1354034-C |
| SNPs | rs1354034 |
| Merged | 0 |
| SNP id current | 1354034 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 3E-54 |
| Pvalue mlog | 53.5228787452803 |
| P value text | |
| Or beta | 6.848 |
| %95 Ci | [5.98-7.71] 10^9/l increase |
| Platform | Affymetrix, Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | platelet count |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004309 |
| Study accession | GCST001337 |
| PubMed ID | 24026423 |
| Journal | Hum Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24026423 |
| Study | A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. |
| Disease/Trait | Platelet count |
| Initial sample | 13,582 European ancestry individuals |
| Replication sample | NA |
| Region | 3p14.3 |
| Chromosome id | chr3 |
| Chromosome position | 56815721 |
| Reported gene | ARHGEF3 |
| Mapped gene | ARHGEF3 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 50650 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1354034-T |
| SNPs | rs1354034 |
| Merged | 0 |
| SNP id current | 1354034 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.61 |
| P value | 6E-24 |
| Pvalue mlog | 23.2218487496163 |
| P value text | |
| Or beta | 7.97 |
| %95 Ci | [NR] unit increase |
| Platform | Illumina [476395] |
| CNV | N |
| Mapped trait | platelet count |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004309 |
| Study accession | GCST002186 |
| PubMed ID | 24026423 |
| Journal | Hum Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/24026423 |
| Study | A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. |
| Disease/Trait | Mean platelet volume |
| Initial sample | 6,291 European ancestry individuals |
| Replication sample | NA |
| Region | 3p14.3 |
| Chromosome id | chr3 |
| Chromosome position | 56815721 |
| Reported gene | ARHGEF3 |
| Mapped gene | ARHGEF3 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 50650 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1354034-C |
| SNPs | rs1354034 |
| Merged | 0 |
| SNP id current | 1354034 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.61 |
| P value | 9E-34 |
| Pvalue mlog | 33.0457574905606 |
| P value text | |
| Or beta | 0.19 |
| %95 Ci | [NR] unit decrease |
| Platform | Illumina [476395] |
| CNV | N |
| Mapped trait | mean platelet volume |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004584 |
| Study accession | GCST002184 |
| PubMed ID | 23263863 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23263863 |
| Study | GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children. |
| Disease/Trait | Platelet count |
| Initial sample | 7,943 African American children, 6,234 European ancestry children |
| Replication sample | NA |
| Region | 3p14.3 |
| Chromosome id | chr3 |
| Chromosome position | 56815721 |
| Reported gene | ARHGEF3 |
| Mapped gene | ARHGEF3 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 50650 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1354034-C |
| SNPs | rs1354034 |
| Merged | 0 |
| SNP id current | 1354034 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.27 |
| P value | 0.0000000000009 |
| Pvalue mlog | 12.0457574905606 |
| P value text | (AA) |
| Or beta | 11.44 |
| %95 Ci | [8.31-14.57] unit increase |
| Platform | Illumina [544917] |
| CNV | N |
| Mapped trait | platelet count |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004309 |
| Study accession | GCST001783 |
| PubMed ID | 23263863 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23263863 |
| Study | GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children. |
| Disease/Trait | Platelet count |
| Initial sample | 7,943 African American children, 6,234 European ancestry children |
| Replication sample | NA |
| Region | 3p14.3 |
| Chromosome id | chr3 |
| Chromosome position | 56815721 |
| Reported gene | ARHGEF3 |
| Mapped gene | ARHGEF3 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 50650 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1354034-T |
| SNPs | rs1354034 |
| Merged | 0 |
| SNP id current | 1354034 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.4092 |
| P value | 0.000000004 |
| Pvalue mlog | 8.39794000867203 |
| P value text | (EA) |
| Or beta | 9.443 |
| %95 Ci | [6.3-12.59] unit decrease |
| Platform | Illumina [544917] |
| CNV | N |
| Mapped trait | platelet count |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004309 |
| Study accession | GCST001783 |
| PubMed ID | 23263863 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23263863 |
| Study | GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children. |
| Disease/Trait | Platelet count |
| Initial sample | 7,943 African American children, 6,234 European ancestry children |
| Replication sample | NA |
| Region | 3p14.3 |
| Chromosome id | chr3 |
| Chromosome position | 56815721 |
| Reported gene | ARHGEF3 |
| Mapped gene | ARHGEF3 |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 50650 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1354034-T |
| SNPs | rs1354034 |
| Merged | 0 |
| SNP id current | 1354034 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | NR |
| P value | 1E-19 |
| Pvalue mlog | 19 |
| P value text | |
| Or beta | 10.4352 |
| %95 Ci | [8.18-12.69] unit decrease |
| Platform | Illumina [544917] |
| CNV | N |
| Mapped trait | platelet count |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004309 |
| Study accession | GCST001783 |
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and Xi'an University of Technology ©2014-2017 All Rights Reserved.
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