Recovery of known associations.

The column “Genes” provides the number of genes in the locus; “SNPs” is the number of SNPs; “Tests” is the number of effective tests corrected for linkage disequilibrium within the locus; “K” is the number of SNPs in the model for GWiS and LASSO; and “SI” is the selection index for LASSO. The genome-wide significance threshold for each method is shown in parentheses next to the method name. The p-values for GWiS, minSNP-P, BIMBAM and VEGAS are gene-based; p-values for minSNP are SNP-based; and Selection Indices for LASSO are genome-wide. For each method, genome-wide significant findings are in bold. Blank entries for GWiS and LASSO indicate that no SNPs were added to the model for these loci. No SNPs within 200 kb of known loci for PR (TBX5-TBX3) and QT (KCNJ2) are genome-wide significant, and these loci are excluded from the table.