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SNP Detail For rs1050828
1.Mapping Information
| Human SNP ID | rs1050828 |
|---|---|
| Human chromosome | chrX |
| Human SNP position | 154536002 |
| Pig chromosome | chrX |
| Pig SNP position | 143501982 |
2.Annotation Information
| PubMed ID | 23446634 |
|---|---|
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23446634 |
| Study | Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network. |
| Disease/Trait | Red blood cell traits |
| Initial sample | Up to 16,485 African American individuals |
| Replication sample | 9,692 African American individuals, 21,020 European ancestry individuals, 14,088 Japanese ancestry individuals |
| Region | Xq28 |
| Chromosome id | chrX |
| Chromosome position | 154536002 |
| Reported gene | F8, CTAG2, G6PD, MECP2, MPP1 |
| Mapped gene | G6PD |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2539 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1050828-T |
| SNPs | rs1050828 |
| Merged | 0 |
| SNP id current | 1050828 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.108 |
| P value | 4E-19 |
| Pvalue mlog | 18.397940008672 |
| P value text | (RBC, AA) |
| Or beta | 0.108 |
| %95 Ci | [0.0063-0.2097] x10^6/uL, decrease |
| Platform | Affymetrix, Illumina [NR] |
| CNV | N |
| Mapped trait | erythrocyte count |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004305 |
| Study accession | GCST001873 |
| PubMed ID | 23446634 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23446634 |
| Study | Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network. |
| Disease/Trait | Red blood cell traits |
| Initial sample | Up to 16,485 African American individuals |
| Replication sample | 9,692 African American individuals, 21,020 European ancestry individuals, 14,088 Japanese ancestry individuals |
| Region | Xq28 |
| Chromosome id | chrX |
| Chromosome position | 154536002 |
| Reported gene | G6PD |
| Mapped gene | G6PD |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2539 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1050828-T |
| SNPs | rs1050828 |
| Merged | 0 |
| SNP id current | 1050828 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.116 |
| P value | 0.00000000002 |
| Pvalue mlog | 10.698970004336 |
| P value text | (RDW, AA) |
| Or beta | 0.0326 |
| %95 Ci | [0.023-0.042] % decrease |
| Platform | Affymetrix, Illumina [NR] |
| CNV | N |
| Mapped trait | red blood cell distribution width |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0005192 |
| Study accession | GCST001873 |
| PubMed ID | 23696099 |
| Journal | G3 (Bethesda) |
| Link | www.ncbi.nlm.nih.gov/pubmed/23696099 |
| Study | Genetic variants that confer resistance to malaria are associated with red blood cell traits in African-Americans: an electronic medical record-based genome-wide association study. |
| Disease/Trait | Red blood cell traits |
| Initial sample | 1904 African American individuals |
| Replication sample | 411 African American individuals |
| Region | Xq28 |
| Chromosome id | chrX |
| Chromosome position | 154536002 |
| Reported gene | G6PD |
| Mapped gene | G6PD |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2539 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1050828-A |
| SNPs | rs1050828 |
| Merged | 0 |
| SNP id current | 1050828 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.12 |
| P value | 0.0000000000004 |
| Pvalue mlog | 12.397940008672 |
| P value text | (RBC count) |
| Or beta | 0.2 |
| %95 Ci | [0.14-0.26] x10^12/L decrease |
| Platform | Illumina [907954] |
| CNV | N |
| Mapped trait | erythrocyte count |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004305 |
| Study accession | GCST002027 |
| PubMed ID | 23696099 |
| Journal | G3 (Bethesda) |
| Link | www.ncbi.nlm.nih.gov/pubmed/23696099 |
| Study | Genetic variants that confer resistance to malaria are associated with red blood cell traits in African-Americans: an electronic medical record-based genome-wide association study. |
| Disease/Trait | Red blood cell traits |
| Initial sample | 1904 African American individuals |
| Replication sample | 411 African American individuals |
| Region | Xq28 |
| Chromosome id | chrX |
| Chromosome position | 154536002 |
| Reported gene | G6PD |
| Mapped gene | G6PD |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2539 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1050828-A |
| SNPs | rs1050828 |
| Merged | 0 |
| SNP id current | 1050828 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.12 |
| P value | 0.00000000000001 |
| Pvalue mlog | 14 |
| P value text | (MCV) |
| Or beta | 2.46 |
| %95 Ci | [1.83-3.09] fL increase |
| Platform | Illumina [907954] |
| CNV | N |
| Mapped trait | mean corpuscular volume |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004526 |
| Study accession | GCST002027 |
| PubMed ID | 23696099 |
| Journal | G3 (Bethesda) |
| Link | www.ncbi.nlm.nih.gov/pubmed/23696099 |
| Study | Genetic variants that confer resistance to malaria are associated with red blood cell traits in African-Americans: an electronic medical record-based genome-wide association study. |
| Disease/Trait | Red blood cell traits |
| Initial sample | 1904 African American individuals |
| Replication sample | 411 African American individuals |
| Region | Xq28 |
| Chromosome id | chrX |
| Chromosome position | 154536002 |
| Reported gene | G6PD |
| Mapped gene | G6PD |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 2539 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs1050828-A |
| SNPs | rs1050828 |
| Merged | 0 |
| SNP id current | 1050828 |
| Context | missense_variant |
| Intergenic | 0 |
| Allele frequency | 0.12 |
| P value | 0.000000009 |
| Pvalue mlog | 8.04575749056067 |
| P value text | (MCH) |
| Or beta | 0.72 |
| %95 Ci | [0.48-0.96] pg increase |
| Platform | Illumina [907954] |
| CNV | N |
| Mapped trait | mean corpuscular hemoglobin |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004527 |
| Study accession | GCST002027 |
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