We also performed an analysis controlling for haplotpyes E-1p. To avoid uncertainty in the phase, we restricted this analysis to samples homozygous for the risk alleles defining E-1p. In Table 3 we report association results of Fisher’s exact test for 10 SNPs which associated with p-value p<10−3 within samples of this subset. It is clear that controlling for E-1p falls far from explaining the large disparity observed for variants within APOL1.
