We estimated the proportion of variance explained by the set of all conditionally independently associated variants. The joint effects of variants in a locus were approximated by β→^JOINT=VMETA−1U→META, where U→META is the single variant score statistics and VMETA is the covariance matrix between them. The phenotypic variance explained by the independently associated variants in a locus is given by β→^jointTcov(G)β→^JOINT, where cov(G) is the genotype covariance estimated from the Haplotype Reference Consortium panel.
