Table 2.

SNPs with the highest population differentiation between Yoruba and Luhya

ChromosomersIDNCBI36/HG18NCBI37/HG19Ref.Alt.YRILWKP valueGene
chr22rs738853193499185236661906AG0.380.055.11E-07APOL1
chr3rs7649861145653390144170700AG0.150.535.49E-07
chr7rs69443027994282780104891CT0.480.115.96E-07CD36
chr5rs6879787141817918141837734TG0.2601.98E-06
chr7rs69679657940401479566078TC0.370.076.04E-06CD36
chr18rs5691765399837855847380CT0.310.048.58E-06
chr7rs69497617934729979509363CT0.40.099.64E-06CD36
chr6rs30941592994381329835834GA0.530.851.15E-05HLA
chr6rs31327122994900029841021AG0.530.851.15E-05HLA
chr6rs31156192995085829842879AG0.530.851.15E-05HLA
  • Frequencies of >1.4 million SNPs were tested in Yoruba (Nigeria) and Luhya (Kenya), two tribes with very high genetic similarity (Fst = 0.008). The 10 most differentiated SNPs after modeling genetic drift and sampling variance are shown here, with G1 showing the strongest statistical evidence for differentiation among all SNPs tested. Alt., alternate allele; LWK, Luhya; NCBI/HG, genomic location; Ref., reference allele; rsID, SNP ID; YRI, Yoruba.