Human SNP ID | rs1427407 |
---|---|
Human chromosome | chr2 |
Human SNP position | 60490908 |
Pig chromosome | chr3 |
Pig SNP position | 85345421 |
PubMed ID | 17767159 |
---|---|
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/17767159 |
Study | A QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15. |
Disease/Trait | F-cell distribution |
Initial sample | 179 European ancestry individuals |
Replication sample | 90 European ancestry individuals |
Region | 2p16.1 |
Chromosome id | chr2 |
Chromosome position | 60490908 |
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 | rs1427407-? |
SNPs | rs1427407 |
Merged | 0 |
SNP id current | 1427407 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.14 |
P value | 6E-31 |
Pvalue mlog | 30.2218487496163 |
P value text | |
Or beta | 13.1 |
%95 Ci | [NR] % variance |
Platform | Illumina [308015] |
CNV | N |
Mapped trait | fetal hemoglobin measurement |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004576 |
Study accession | GCST000069 |
PubMed ID | 25372704 |
Journal | PLoS One |
Link | www.ncbi.nlm.nih.gov/pubmed/25372704 |
Study | Genome wide association study of fetal hemoglobin in sickle cell anemia in Tanzania. |
Disease/Trait | Fetal hemoglobin levels in sickle cell anemia |
Initial sample | 1,213 Tanzanian ancestry cases |
Replication sample | 321 Afro-Caribbean and Sub-Saharan African cases |
Region | 2p16.1 |
Chromosome id | chr2 |
Chromosome position | 60490908 |
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 | rs1427407-? |
SNPs | rs1427407 |
Merged | 0 |
SNP id current | 1427407 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.78 |
P value | 4E-53 |
Pvalue mlog | 52.397940008672 |
P value text | |
Or beta | 0.3 |
%95 Ci | [NR] unit decrease |
Platform | Illumina [15153765] (imputed) |
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 | GCST002687 |
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 |