phenotypic variance of rheumatoid arthritis and type 1 diabetes, respectively (as described in the Supplementary Note). As a result, the genomic control λ increased to 0.989 for rheumatoid arthritis and 0.991 for type 1 diabetes. We performed this conditioning procedure only for estimating variance parameters and not in the SNP association test so that the P values would be consistent with the unconditioned analysis. Conditioning on the SNPs with such a strong effect may further improve the power to identify novel loci. A more sophisticated conditional analysis—for example, one including haplotype effects or epistatic interactions into covariates—may also better account for the strong effects in the autoimmune diseases37.
