In order to study the effect of highly associated SNPs (e.g. SNPs in MHC regions for immune traits), we repeated the analysis on CD, RA, BC and T2D after removing the SNPs in MHC region (chr6: 28,477,797–33,448,354 bp). Re-analysis of CEL was unnecessary since the training summary statistics of CEL does not contain any SNP in the MHC region. After removing SNPs in MHC regions, the prediction accuracies for RA drops dramatically for all methods and AnnoPred remained to be the method with the best performance (S9 Table). For the rest diseases, results varied little from the original analysis. Besides COR, we also included AUCs for all the analysis performed (S2, S6, S9 and S10 Tables), all of which showed consistent patterns.
