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SNP Detail For rs11886868
1.Mapping Information
| Human SNP ID | rs11886868 |
|---|---|
| Human chromosome | chr2 |
| Human SNP position | 60493111 |
| Pig chromosome | chr3 |
| Pig SNP position | 85343894 |
2.Annotation Information
| PubMed ID | 18245381 |
|---|---|
| Journal | Proc Natl Acad Sci U S A |
| Link | www.ncbi.nlm.nih.gov/pubmed/18245381 |
| Study | Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia. |
| Disease/Trait | Fetal hemoglobin levels |
| Initial sample | 4,305 European ancestry individuals |
| Replication sample | 521 European ancestry individuals |
| Region | 2p16.1 |
| Chromosome id | chr2 |
| Chromosome position | 60493111 |
| Reported gene | BCL11A |
| Mapped gene | BCL11A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | 53335 |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs11886868-T |
| SNPs | rs11886868 |
| Merged | 0 |
| SNP id current | 11886868 |
| Context | intron_variant |
| Intergenic | 0 |
| Allele frequency | 0.8 |
| P value | 7E-35 |
| Pvalue mlog | 34.1549019599857 |
| P value text | |
| Or beta | 0.48 |
| %95 Ci | [NR] s.d. decrease in HbF |
| Platform | Affymetrix [362129] |
| CNV | N |
| Mapped trait | fetal hemoglobin measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004576 |
| Study accession | GCST000150 |
| PubMed ID | 21326311 |
| Journal | J Hum Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21326311 |
| Study | Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients. |
| Disease/Trait | F-cell distribution |
| Initial sample | 440 African American individuals |
| Replication sample | NA |
| Region | 2p16.1 |
| Chromosome id | chr2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2 |
| Chromosome position | 60494212;60492835;60496952;60493622;60493454;60493111;60496131;60494176;60491212;60498316;60495106;60490908;60491939;60487726;60493816;60496537;60488044;60496951;60486100;60494905 |
| Reported gene | BCL11A |
| Mapped gene | BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs7557939-?; rs766432-?; rs1896296-?; rs10172646-?; rs10195871-?; rs11886868-?; rs7565301-?; rs7584113-?; rs7599488-?; rs7606173-?; rs6738440-?; rs1427407-?; rs1896294-?; rs6545816-?; rs4671393-?; rs6729815-?; rs6545817-?; rs1896295-?; rs10189857-?; rs670 |
| SNPs | rs7557939; rs766432; rs1896296; rs10172646; rs10195871; rs11886868; rs7565301; rs7584113; rs7599488; rs7606173; rs6738440; rs1427407; rs1896294; rs6545816; rs4671393; rs6729815; rs6545817; rs1896295; rs10189857; rs6706648 |
| Merged | 0 |
| SNP id current | |
| Context | intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; |
| Intergenic | |
| Allele frequency | 0.42 |
| P value | 0.0000002 |
| Pvalue mlog | 6.69897000433601 |
| P value text | |
| Or beta | 1.07 |
| %95 Ci | [0.68-1.46] unit increase |
| Platform | Illumina [660740] |
| CNV | N |
| Mapped trait | fetal hemoglobin measurement, Sickle cell anemia |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004576, http://www.orpha.net/ORDO/Orphanet_232 |
| Study accession | GCST000982 |
| PubMed ID | 21326311 |
| Journal | J Hum Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21326311 |
| Study | Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients. |
| Disease/Trait | F-cell distribution |
| Initial sample | 440 African American individuals |
| Replication sample | NA |
| Region | 2p16.1 |
| Chromosome id | chr2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2 |
| Chromosome position | 60494212;60492835;60496952;60493622;60493454;60493111;60496131;60494176;60491212;60498316;60495106;60490908;60491939;60487726;60493816;60496537;60488044;60496951;60486100;60494905 |
| Reported gene | BCL11A |
| Mapped gene | BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A; BCL11A |
| Upstream gene id | |
| Downstream gene id | |
| SNP gene ids | |
| Upstream gene distance | |
| Downstream gene distance | |
| SNP risk allele | rs7557939-?; rs766432-?; rs1896296-?; rs10172646-?; rs10195871-?; rs11886868-?; rs7565301-?; rs7584113-?; rs7599488-?; rs7606173-?; rs6738440-?; rs1427407-?; rs1896294-?; rs6545816-?; rs4671393-?; rs6729815-?; rs6545817-?; rs1896295-?; rs10189857-?; rs670 |
| SNPs | rs7557939; rs766432; rs1896296; rs10172646; rs10195871; rs11886868; rs7565301; rs7584113; rs7599488; rs7606173; rs6738440; rs1427407; rs1896294; rs6545816; rs4671393; rs6729815; rs6545817; rs1896295; rs10189857; rs6706648 |
| Merged | 0 |
| SNP id current | |
| Context | intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; intron_variant; |
| Intergenic | |
| Allele frequency | 0.254 |
| P value | 0.0000000000000002 |
| Pvalue mlog | 15.698970004336 |
| P value text | |
| Or beta | 1.98 |
| %95 Ci | [1.57-2.39] unit increase |
| Platform | Illumina [660740] |
| CNV | N |
| Mapped trait | fetal hemoglobin measurement, Sickle cell anemia |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004576, http://www.orpha.net/ORDO/Orphanet_232 |
| Study accession | GCST000982 |
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