SNP Detail For rs1427407
1.Mapping Information
Human SNP ID rs1427407
Human chromosome chr2
Human SNP position 60490908
Pig chromosome chr3
Pig SNP position 85345421
2.Annotation Information
PubMed ID17767159
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/17767159
StudyA QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15.
Disease/TraitF-cell distribution
Initial sample179 European ancestry individuals
Replication sample90 European ancestry individuals
Region2p16.1
Chromosome idchr2
Chromosome position60490908
Reported geneBCL11A
Mapped geneBCL11A
Upstream gene id
Downstream gene id
SNP gene ids53335
Upstream gene distance
Downstream gene distance
SNP risk allelers1427407-?
SNPsrs1427407
Merged0
SNP id current1427407
Contextintron_variant
Intergenic0
Allele frequency0.14
P value6E-31
Pvalue mlog30.2218487496163
P value text
Or beta13.1
%95 Ci[NR] % variance
PlatformIllumina [308015]
CNVN
Mapped traitfetal hemoglobin measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004576
Study accessionGCST000069
PubMed ID25372704
JournalPLoS One
Linkwww.ncbi.nlm.nih.gov/pubmed/25372704
StudyGenome wide association study of fetal hemoglobin in sickle cell anemia in Tanzania.
Disease/TraitFetal hemoglobin levels in sickle cell anemia
Initial sample1,213 Tanzanian ancestry cases
Replication sample321 Afro-Caribbean and Sub-Saharan African cases
Region2p16.1
Chromosome idchr2
Chromosome position60490908
Reported geneBCL11A
Mapped geneBCL11A
Upstream gene id
Downstream gene id
SNP gene ids53335
Upstream gene distance
Downstream gene distance
SNP risk allelers1427407-?
SNPsrs1427407
Merged0
SNP id current1427407
Contextintron_variant
Intergenic0
Allele frequency0.78
P value4E-53
Pvalue mlog52.397940008672
P value text
Or beta0.3
%95 Ci[NR] unit decrease
PlatformIllumina [15153765] (imputed)
CNVN
Mapped traitfetal hemoglobin measurement, Sickle cell anemia
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004576, http://www.orpha.net/ORDO/Orphanet_232
Study accessionGCST002687
PubMed ID21326311
JournalJ Hum Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21326311
StudyGenome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients.
Disease/TraitF-cell distribution
Initial sample440 African American individuals
Replication sampleNA
Region2p16.1
Chromosome idchr2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2
Chromosome position60494212;60492835;60496952;60493622;60493454;60493111;60496131;60494176;60491212;60498316;60495106;60490908;60491939;60487726;60493816;60496537;60488044;60496951;60486100;60494905
Reported geneBCL11A
Mapped geneBCL11A; 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 allelers7557939-?; rs766432-?; rs1896296-?; rs10172646-?; rs10195871-?; rs11886868-?; rs7565301-?; rs7584113-?; rs7599488-?; rs7606173-?; rs6738440-?; rs1427407-?; rs1896294-?; rs6545816-?; rs4671393-?; rs6729815-?; rs6545817-?; rs1896295-?; rs10189857-?; rs670
SNPsrs7557939; rs766432; rs1896296; rs10172646; rs10195871; rs11886868; rs7565301; rs7584113; rs7599488; rs7606173; rs6738440; rs1427407; rs1896294; rs6545816; rs4671393; rs6729815; rs6545817; rs1896295; rs10189857; rs6706648
Merged0
SNP id current
Contextintron_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 frequency0.42
P value0.0000002
Pvalue mlog6.69897000433601
P value text
Or beta1.07
%95 Ci[0.68-1.46] unit increase
PlatformIllumina [660740]
CNVN
Mapped traitfetal hemoglobin measurement, Sickle cell anemia
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004576, http://www.orpha.net/ORDO/Orphanet_232
Study accessionGCST000982
PubMed ID21326311
JournalJ Hum Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21326311
StudyGenome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients.
Disease/TraitF-cell distribution
Initial sample440 African American individuals
Replication sampleNA
Region2p16.1
Chromosome idchr2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2
Chromosome position60494212;60492835;60496952;60493622;60493454;60493111;60496131;60494176;60491212;60498316;60495106;60490908;60491939;60487726;60493816;60496537;60488044;60496951;60486100;60494905
Reported geneBCL11A
Mapped geneBCL11A; 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 allelers7557939-?; rs766432-?; rs1896296-?; rs10172646-?; rs10195871-?; rs11886868-?; rs7565301-?; rs7584113-?; rs7599488-?; rs7606173-?; rs6738440-?; rs1427407-?; rs1896294-?; rs6545816-?; rs4671393-?; rs6729815-?; rs6545817-?; rs1896295-?; rs10189857-?; rs670
SNPsrs7557939; rs766432; rs1896296; rs10172646; rs10195871; rs11886868; rs7565301; rs7584113; rs7599488; rs7606173; rs6738440; rs1427407; rs1896294; rs6545816; rs4671393; rs6729815; rs6545817; rs1896295; rs10189857; rs6706648
Merged0
SNP id current
Contextintron_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 frequency0.254
P value0.0000000000000002
Pvalue mlog15.698970004336
P value text
Or beta1.98
%95 Ci[1.57-2.39] unit increase
PlatformIllumina [660740]
CNVN
Mapped traitfetal hemoglobin measurement, Sickle cell anemia
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004576, http://www.orpha.net/ORDO/Orphanet_232
Study accessionGCST000982