Table 5: Replicability analysis for Example 2 in Section 5: GWAS of Crohns disease. The number of SNPs in the primary study was 635,547, and 126 SNPs were followed- up. The 36 discoveries by Procedure 3.2 with parameters ( q$_{1}$, q ) = (0 . 04 , 0 . 05) are listed according to the adjusted p -values. The primary and follow-up studies p -values are given in columns 4 and 5; the adjusted p -values for c = 0 . 8 are given in column 6 for Procedure 3.2, and in column 7 for the modification of item 1 in Theorem 3.3. Index Chromosome Position p$_{1}$ p$_{2}$ p REPadj FDR ˜ p REPadj FDR 1 1 67417979 3.19e-34 1.5e-36 2.53e-28 3.53e-27 2 1 67414547 5.05e-36 3.1e-29 9.69e-27 9.69e-27 3 1 67387537 1.35e-24 5.62e-17 1.17e-14 1.17e-14 4 2 233962410 5.66e-21 7.67e-14 1.2e-11 1.2e-11 5 10 64108492 9.51e-12 1.61e-10 1.51e-06 1.5e-05 6 5 40428485 2.51e-22 2.79e-08 2.84e-06 3.31e-06 7 5 40437266 2.26e-22 3.18e-08 2.84e-06 3.31e-06 8 10 101281583 8.53e-11 1.69e-07 1.32e-05 7.74e-05 9 18 12769947 5.95e-12 2.41e-07 1.61e-05 1.88e-05 10 5 150239060 3.18e-11 2.57e-07 1.61e-05 3.91e-05 11 10 101282445 9.09e-11 3.1e-07 1.76e-05 7.74e-05 12 5 150203580 4.09e-11 7.47e-07 3.89e-05 4.67e-05 13 18 12799340 3.27e-11 1.23e-06 5.91e-05 6.99e-05 14 5 131798704 2.29e-09 3.52e-11 0.00013 0.00169 15 5 158747111 4.4e-09 3.66e-06 0.000233 0.00305 16 2 233965368 1.28e-21 3.66e-05 0.00143 0.00163 17 13 43355925 8.04e-08 1.33e-07 0.00376 0.0469 18 12 39104262 8.95e-08 6.55e-05 0.00395 0.0496 19 3 49676987 9.47e-08 2.24e-06 0.00396 0.0499 20 3 49696536 1.08e-07 5.64e-07 0.00429 0.0544 21 12 38888207 6.64e-08 0.000165 0.00491 0.0433 22 6 167408399 1.65e-07 3.26e-07 0.00596 0.0731 23 9 114645994 1.96e-07 6.58e-05 0.00677 0.0768 24 6 20836710 1.26e-07 0.000278 0.00724 0.0607 25 1 169593891 2.01e-07 0.000321 0.00802 0.0768 26 1 197667523 3.41e-07 2.34e-06 0.01 0.111 27 9 4971602 3.4e-07 0.00043 0.01 0.111 28 1 157665119 1.75e-07 0.000481 0.0107 0.0745 29 11 75978964 7.16e-08 0.000732 0.0158 0.044 30 20 61798026 7.6e-07 0.000138 0.0201 0.234 31 6 167405736 1.65e-07 0.00121 0.0241 0.0731 32 1 197691964 9.69e-07 1e-04 0.0241 0.29 33 17 35294289 1.06e-06 0.000292 0.0255 0.308 34 8 126603853 1.9e-06 0.000182 0.0431 0.457 35 6 106541962 1.85e-06 7.7e-06 0.0431 0.457 36 9 4978761 1.96e-06 0.00162 0.0433 0.462 34