A locus was defined as a 1MB region surrounding the “sentinel” variant (the variant in the locus with the lowest p-value). When any two such loci overlapped or abutted, they were collapsed into a single locus. Variants within each locus were subjected to conditional analysis using a novel partial correlation-based score statistic using cohort-level summary statistics57 implemented in a sequential forward selection framework. The method requires marginal association statistics and approximated covariance matrices among them, and performs favorably compared to existing methods57 (Supplementary Table 24). Covariances among effects were based upon the linkage disequilibrium information estimated from a subset of the Haplotype Reference Consortium41.
