To evaluate the extent to which prediction was driven by these significant hits, we split each model into two models without any refitting of the coefficients; a model excluding all SNPs with single-SNP P<5×10−7 as well as any SNPs in LD with these (); specifically for T1D and RA we also removed any SNPs that mapped to the MHC gene clusters in chromosome 6 [42] and a model with only these excluded SNPs. This evidence concerns the gene HLA-C and type 1 diabetes mellitus.