******************************************************** * * * ANALYSIS OF SNP-DISEASE ASSOCIATION * * IN CASE-CONTROL STUDIES * * WITH POTENTIALLY MISSING GENOTYPE DATA * * * ******************************************************** Sample Size of Case-Control Study : 2000 Number of SNPs in Case-Control Study: 100 Number of Trios in Reference Panel: 30 Number of SNPs in Reference Panel : 562 Phased Genotypes: available Number of SNPs in Phased Genotypes: 428 Mode of Inheritance: additive Typed SNP_id position 1/0 M_D Freq log(OR) std_error test_stat p-value ------ ---------- -------- --- ------ ------ -------- --------- --------- --------- 1.0000 rs3892957 53295262 A/G - 0.2218 0.1116 0.0757 1.4745 1.40e-01 1.0000 rs570046 53295430 A/G - 0.7742 -0.1267 0.0751 -1.6873 9.15e-02 1.0000 rs3894276 53295746 A/G - 0.2233 0.1394 0.0756 1.8464 6.48e-02 no rs12963672 53295932 A/T 0.4068 0.0222 0.8512 0.3689 2.3072 2.10e-02 no rs12455210 53296375 A/G 0.9165 0.6910 -0.0571 0.0764 -0.7480 4.54e-01 no rs7237996 53296505 A/G 0.8545 0.7333 -0.0825 0.0800 -1.0321 3.02e-01 no rs504442 53296545 G/T 0.8034 0.9326 0.2369 0.3496 0.6777 4.98e-01 no rs12963089 53296763 C/G 0.9739 0.6897 0.0272 0.0680 0.3993 6.90e-01 1.0000 rs660936 53297068 A/T - 0.6863 0.0203 0.0672 0.3024 7.62e-01 no rs17758515 53297451 C/T 0.9735 0.7000 0.0318 0.0713 0.4455 6.56e-01 no rs562330 53297680 A/G 0.3277 0.0111 - - - - 1.0000 rs674849 53297884 C/T - 0.2772 0.0025 0.0702 0.0351 9.72e-01 no rs17831587 53298886 A/C 0.3277 0.9886 - - - - no rs10503013 53299859 A/T 0.3277 0.9889 - - - - 0.9700 rs615030 53300352 C/T - 0.7054 -0.0033 0.0696 -0.0480 9.62e-01 1.0000 rs629737 53301269 A/C - 0.6985 0.0142 0.0687 0.2062 8.37e-01 no rs630250 53301411 C/T 1.0000 0.3111 -0.0355 0.0686 -0.5183 6.04e-01 no rs9789131 53301555 G/T 1.0000 0.3090 -0.0355 0.0686 -0.5183 6.04e-01 1.0000 rs519596 53302863 A/G - 0.3033 -0.0212 0.0687 -0.3092 7.57e-01 no rs11665166 53302995 A/G 0.8276 0.9722 0.0328 0.1796 0.1825 8.55e-01 no rs658446 53303141 A/G 1.0000 0.0706 -0.1895 0.2712 -0.6987 4.85e-01 no rs11152015 53303182 C/T 1.0000 0.9500 0.0994 0.1669 0.5954 5.52e-01 1.0000 rs660626 53303627 C/T - 0.7278 -0.0230 0.0714 -0.3214 7.48e-01 1.0000 rs3745070 53303942 C/T - 0.9640 0.0836 0.1671 0.5006 6.17e-01 no rs3745067 53304279 C/G 0.8906 0.8444 -0.0430 0.0814 -0.5281 5.97e-01 no rs3745066 53304369 C/T 0.5868 0.0625 0.1758 0.1120 1.5694 1.17e-01 1.0000 rs3745064 53305064 C/T - 0.6797 -0.0158 0.0672 -0.2354 8.14e-01 0.9490 rs3848516 53306378 A/G - 0.3140 -0.0006 0.0701 -0.0083 9.93e-01 0.9990 rs608017 53306709 C/G - 0.6864 -0.0093 0.0683 -0.1366 8.91e-01 0.9995 rs608823 53306868 A/G - 0.3134 0.0108 0.0683 0.1582 8.74e-01 no rs12607294 53307854 C/T 1.0000 0.0500 -0.0994 0.1669 -0.5954 5.52e-01 1.0000 rs552396 53308810 G/T - 0.6870 -0.0229 0.0677 -0.3386 7.35e-01 0.9010 rs2279096 53308956 A/G - 0.6898 -0.0325 0.0722 -0.4504 6.52e-01 no rs2279099 53309107 C/T 1.0000 0.9500 0.0994 0.1669 0.5954 5.52e-01 1.0000 rs1217583 53310272 C/T - 0.8552 -0.1503 0.0903 -1.6658 9.58e-02 no rs683572 53310672 C/T 0.6711 0.0183 -0.0766 0.3385 -0.2263 8.21e-01 1.0000 rs3899444 53310926 A/G - 0.3225 0.0678 0.0672 1.0079 3.14e-01 no rs686703 53311380 A/C 0.2593 0.0123 0.0121 0.3340 0.0364 9.71e-01 no rs10503014 53311630 C/T 1.0000 0.1722 -0.0195 0.0761 -0.2567 7.97e-01 1.0000 rs4940796 53311675 C/T - 0.9637 -0.0144 0.1700 -0.0850 9.32e-01 no rs4940797 53311781 C/T 1.0000 0.9602 0.0994 0.1669 0.5954 5.52e-01 no rs3894277 53312378 A/G 0.2167 0.0625 0.1786 0.1909 0.9353 3.50e-01 no rs12454101 53312467 A/G 1.0000 0.0500 -0.0994 0.1669 -0.5954 5.52e-01 1.0000 rs542856 53312632 A/G - 0.1477 -0.0685 0.0898 -0.7630 4.45e-01 no rs7229018 53312780 C/G 0.7117 0.9278 -0.0378 0.1874 -0.2018 8.40e-01 no rs7229750 53312878 A/G 0.8134 0.6080 0.0223 0.0805 0.2775 7.81e-01 no rs7233335 53313162 C/G 1.0000 0.8056 0.1285 0.0791 1.6237 1.04e-01 no rs4940804 53313517 C/T 1.0000 0.8056 0.1285 0.0791 1.6237 1.04e-01 1.0000 rs644016 53315545 C/T - 0.6685 0.0092 0.0679 0.1359 8.92e-01 no rs8099803 53315572 A/G 1.0000 0.8556 0.0905 0.0814 1.1111 2.67e-01 no rs6566884 53316077 G/T 1.0000 0.8090 0.1285 0.0791 1.6237 1.04e-01 1.0000 rs3893413 53316543 A/G - 0.8020 0.1215 0.0801 1.5183 1.29e-01 0.9860 rs618218 53316730 A/T - 0.4599 -0.0505 0.0635 -0.7957 4.26e-01 no rs3898924 53317482 A/C 1.0000 0.0500 -0.0994 0.1669 -0.5954 5.52e-01 0.9985 rs585491 53318026 A/C - 0.4607 -0.0505 0.0635 -0.7957 4.26e-01 1.0000 rs4940829 53318383 A/G - 0.7937 0.0327 0.0771 0.4241 6.71e-01 no rs4940833 53318893 A/G 1.0000 0.7965 0.1285 0.0791 1.6237 1.04e-01 no rs4940835 53318945 A/G 1.0000 0.8056 0.1285 0.0791 1.6237 1.04e-01 no rs8098520 53320727 A/G 1.0000 0.8056 0.1285 0.0791 1.6237 1.04e-01 no rs12608302 53320803 A/G 1.0000 0.9500 0.0994 0.1669 0.5954 5.52e-01 no rs12605933 53320911 G/T 1.0000 0.9500 0.0994 0.1669 0.5954 5.52e-01 no rs11662635 53321272 A/G 1.0000 0.0500 -0.0994 0.1669 -0.5954 5.52e-01 no rs7228132 53321367 G/T 1.0000 0.8056 0.1285 0.0791 1.6237 1.04e-01 no rs576678 53323292 A/G 1.0000 0.8176 0.0164 0.0902 0.1814 8.56e-01 no rs1460210 53323310 C/T 0.6711 0.9494 0.3557 0.2242 1.5863 1.13e-01 no rs8095478 53323391 A/G 1.0000 0.3333 -0.0286 0.0683 -0.4195 6.75e-01 no rs617172 53323587 A/G 1.0000 0.1897 -0.0164 0.0902 -0.1814 8.56e-01 no rs602466 53324594 A/T 1.0000 0.1889 -0.0164 0.0902 -0.1814 8.56e-01 no rs17063791 53325766 C/G 1.0000 0.8556 -0.0077 0.0894 -0.0860 9.31e-01 no rs17063792 53325973 A/G 1.0000 0.8556 -0.0077 0.0894 -0.0860 9.31e-01 no rs10503015 53326141 C/T 1.0000 0.8539 -0.0077 0.0894 -0.0860 9.31e-01 no rs12962079 53326208 G/T 1.0000 0.9667 0.0821 0.3075 0.2669 7.90e-01 no rs10503016 53326431 A/G 1.0000 0.0333 -0.0821 0.3075 -0.2669 7.90e-01 no rs10503017 53326687 C/T 1.0000 0.6667 -0.0484 0.0736 -0.6578 5.11e-01 no rs10503018 53326747 A/G 1.0000 0.6667 -0.0484 0.0736 -0.6578 5.11e-01 no rs12968823 53327191 A/T 1.0000 0.9663 0.2007 0.2932 0.6847 4.94e-01 no rs17063802 53327478 A/G 1.0000 0.3333 0.0540 0.0724 0.7461 4.56e-01 no rs17063805 53327961 A/G 1.0000 0.8596 0.0136 0.0882 0.1542 8.77e-01 1.0000 rs3901913 53328091 A/G - 0.3450 0.0130 0.0658 0.1974 8.44e-01 1.0000 rs3901912 53329318 C/T - 0.3450 0.0130 0.0658 0.1974 8.44e-01 no rs3901911 53329366 A/G 1.0000 0.6667 -0.0540 0.0724 -0.7461 4.56e-01 no rs3901910 53329458 C/T 0.9201 0.6512 -0.0443 0.0862 -0.5140 6.07e-01 no rs3901909 53329466 A/G 1.0000 0.0915 -0.0258 0.1634 -0.1579 8.75e-01 no rs3901908 53329484 A/G 1.0000 0.6667 -0.0540 0.0724 -0.7461 4.56e-01 no rs10871746 53329935 C/T 1.0000 0.6629 -0.0540 0.0724 -0.7461 4.56e-01 no rs8089950 53330140 G/T 1.0000 0.6667 -0.0540 0.0724 -0.7461 4.56e-01 no rs8089975 53330223 C/T 1.0000 0.6685 -0.0540 0.0724 -0.7461 4.56e-01 no rs11875972 53331055 A/C 0.9687 0.8444 0.0584 0.1036 0.5637 5.73e-01 no rs17758897 53331130 A/G 1.0000 0.0333 -0.3188 0.4755 -0.6704 5.03e-01 no rs9964234 53331165 A/T 0.9807 0.6722 0.0931 0.0798 1.1674 2.43e-01 no rs4940864 53334033 A/T 1.0000 0.9659 -0.1519 0.2969 -0.5116 6.09e-01 no rs7237956 53334831 A/T 1.0000 0.1056 -0.0392 0.1630 -0.2403 8.10e-01 no rs4422053 53335584 G/T 1.0000 0.0345 0.1513 0.2969 0.5096 6.10e-01 no rs2849425 53335746 A/G 1.0000 0.8652 -0.0213 0.1116 -0.1910 8.49e-01 no rs478683 53335818 C/T 1.0000 0.8611 -0.0213 0.1116 -0.1910 8.49e-01 1.0000 rs510001 53336864 A/G - 0.1295 -0.0852 0.0924 -0.9227 3.56e-01 no rs510086 53336895 A/G 1.0000 0.8722 0.0742 0.0934 0.7944 4.27e-01 no rs6566885 53336928 A/G 1.0000 0.8389 0.0419 0.0907 0.4623 6.44e-01 no rs510999 53337015 C/T 1.0000 0.8722 0.0742 0.0934 0.7944 4.27e-01 1.0000 rs513767 53337337 A/G - 0.0198 0.2844 0.2290 1.2465 2.13e-01 no rs17832002 53337394 A/T 1.0000 0.1056 0.0273 0.1613 0.1693 8.66e-01 no rs7239385 53338154 G/T 0.9270 0.1722 0.0359 0.1062 0.3379 7.35e-01 no rs2849424 53338168 C/G 1.0000 0.1222 -0.1038 0.0984 -1.0547 2.92e-01 1.0000 rs624961 53339916 A/G - 0.6380 0.0696 0.0660 1.0552 2.91e-01 no rs7235134 53340294 C/G 1.0000 0.2557 -0.0305 0.0713 -0.4274 6.69e-01 no rs17832032 53341297 A/G 1.0000 0.9667 0.0987 0.3351 0.2944 7.68e-01 no rs652140 53341398 A/G 1.0000 0.6111 0.0791 0.0671 1.1777 2.39e-01 no rs12954613 53341624 C/T 0.9730 0.4157 0.0270 0.0695 0.3894 6.97e-01 1.0000 rs542233 53341777 A/G - 0.0225 -0.1398 0.2162 -0.6472 5.18e-01 no rs12967876 53342035 A/G 0.9397 0.3988 0.0269 0.0705 0.3814 7.03e-01 no rs1599238 53342611 C/G 0.9730 0.5833 -0.0270 0.0695 -0.3894 6.97e-01 0.9155 rs606145 53344615 A/G - 0.1303 -0.0537 0.0984 -0.5455 5.85e-01 1.0000 rs536170 53345276 A/T - 0.1300 -0.0088 0.0938 -0.0938 9.25e-01 no rs8086569 53346433 C/G 0.9075 0.8278 -0.1929 0.1187 -1.6253 1.04e-01 1.0000 rs1942853 53346679 A/G - 0.9587 -0.0386 0.1605 -0.2407 8.10e-01 no rs473728 53348005 A/G 0.9604 0.2833 -0.0265 0.0812 -0.3269 7.44e-01 no rs7242048 53348805 C/T 1.0000 0.8944 0.1146 0.1654 0.6930 4.88e-01 no rs17752881 53350257 A/G 0.6563 0.8222 0.0784 0.1333 0.5884 5.56e-01 no rs7230083 53351995 C/T 1.0000 0.9329 0.0497 0.0887 0.5606 5.75e-01 1.0000 rs643693 53352051 G/T - 0.0685 0.0774 0.1245 0.6220 5.34e-01 no rs3859415 53352066 A/G 0.8848 0.5783 0.0117 0.0678 0.1727 8.63e-01 0.9800 rs754789 53352459 A/G - 0.8513 0.0734 0.0900 0.8158 4.15e-01 no rs17685679 53354164 C/G 0.8299 0.1011 -0.2306 0.1418 -1.6266 1.04e-01 1.0000 rs613434 53354195 C/T - 0.6700 -0.0224 0.0669 -0.3347 7.38e-01 no rs17752911 53354836 A/C 1.0000 0.5750 0.0104 0.0625 0.1668 8.68e-01 1.0000 rs579643 53354884 C/T - 0.0752 -0.1858 0.1222 -1.5223 1.28e-01 0.9995 rs597741 53355474 A/G - 0.3332 -0.0472 0.0671 -0.7031 4.82e-01 no rs12457388 53356079 A/G 1.0000 0.9943 0.0570 0.3312 0.1721 8.63e-01 no rs17063853 53356562 C/T 0.9459 0.8167 -0.0830 0.1091 -0.7606 4.47e-01 no rs582342 53356573 C/T 1.0000 0.0600 -0.0081 0.1850 -0.0439 9.65e-01 1.0000 rs1531348 53360399 C/T - 0.5188 0.0265 0.0639 0.4152 6.78e-01 1.0000 rs515897 53360504 A/G - 0.6322 -0.0413 0.0659 -0.6260 5.31e-01 no rs7240764 53360815 C/T 1.0000 0.9889 -0.7321 0.3514 -2.0837 3.72e-02 1.0000 rs543259 53361150 C/T - 0.5675 -0.0329 0.0642 -0.5133 6.08e-01 no rs17063854 53361196 A/G 1.0000 0.0278 -0.2295 0.2943 -0.7798 4.36e-01 no rs547968 53361708 A/C 1.0000 0.9833 0.2323 0.1896 1.2254 2.20e-01 0.9975 rs571718 53361951 C/G - 0.2388 0.0188 0.0743 0.2523 8.01e-01 no rs9959170 53362139 A/C 0.8555 0.1000 0.1066 0.1048 1.0172 3.09e-01 no rs9958503 53362220 A/G 0.9353 0.1111 0.0734 0.0930 0.7893 4.30e-01 1.0000 rs13732 53363314 A/C - 0.4923 -0.0417 0.0631 -0.6619 5.08e-01 no rs7238897 53364056 A/C 0.4369 0.7073 0.3516 0.1359 2.5862 9.71e-03 1.0000 rs663774 53364379 G/T - 0.1303 -0.0744 0.0936 -0.7950 4.27e-01 no rs1062010 53366571 A/C 0.5071 0.7722 0.5205 0.1745 2.9825 2.86e-03 no rs8339 53368694 A/G 0.9245 0.1111 -0.3001 0.1166 -2.5736 1.01e-02 no rs8099115 53368825 A/G 1.0000 0.0056 -1.2557 0.6843 -1.8350 6.65e-02 no rs12957678 53369137 C/T 0.8716 0.8580 0.0816 0.1108 0.7365 4.61e-01 no rs11660001 53371227 A/G 0.4857 0.2308 -0.5839 0.1916 -3.0474 2.31e-03 no rs12960608 53371835 A/G 0.5278 0.9831 0.2613 0.3445 0.7585 4.48e-01 no rs1790611 53371994 C/T 0.9756 0.6667 -0.5001 0.0683 -7.3252 2.39e-13 1.0000 rs536560 53372646 C/T - 0.6530 -0.4738 0.0684 -6.9894 2.76e-12 no rs11663133 53374866 C/T 0.3790 0.9828 0.6340 0.5351 1.1848 2.36e-01 1.0000 rs1736442 53376775 A/G - 0.4148 0.4808 0.0660 7.3495 1.99e-13 1.0000 rs1736440 53377252 A/G - 0.4325 0.5089 0.0654 7.8600 3.84e-15 no rs536765 53377381 C/G 1.0000 0.7278 -0.4665 0.0671 -6.9557 3.51e-12 no rs1646594 53377671 A/G 1.0000 0.3444 0.4562 0.0645 7.0696 1.55e-12 no rs1787997 53378056 C/G 1.0000 0.3500 0.4253 0.0686 6.1957 5.80e-10 no rs1790613 53378109 A/G 1.0000 0.3371 0.5258 0.0652 8.0622 7.50e-16 no rs1787998 53378720 A/C 1.0000 0.6647 -0.5258 0.0652 -8.0622 7.50e-16 no rs1626110 53380075 A/G 1.0000 0.0444 -0.2463 0.1460 -1.6863 9.17e-02 no rs1736439 53380893 C/T 1.0000 0.6629 -0.5258 0.0652 -8.0622 7.50e-16 1.0000 rs3817726 53381465 A/G - 0.5795 -0.5100 0.0663 -7.7724 7.70e-15 1.0000 rs1812482 53382598 A/G - 0.4675 0.4584 0.0654 7.0715 1.53e-12 1.0000 rs2040242 53382788 A/C - 0.5925 -0.3647 0.0658 -5.5700 2.55e-08 no rs3753178 53382816 A/G 1.0000 0.9556 0.3102 0.1893 1.6384 1.01e-01 1.0000 rs2269223 53384038 C/T - 0.4068 0.3669 0.0659 5.6027 2.11e-08 1.0000 rs2269222 53384376 A/G - 0.0517 -0.2570 0.1442 -1.7877 7.38e-02 no rs7241377 53386008 G/T 1.0000 0.3333 -0.0107 0.0691 -0.1542 8.77e-01 1.0000 rs1790619 53386275 C/T - 0.6545 0.0171 0.0655 0.2619 7.93e-01 1.0000 rs2269221 53386438 C/T - 0.9025 -0.0476 0.1091 -0.4365 6.62e-01 no rs1736436 53386799 A/G 0.0000 0.0120 - - - - 1.0000 rs1788003 53387293 A/C - 0.6605 0.0693 0.0680 1.0195 3.08e-01 no rs533952 53387340 G/T 0.9248 0.7500 -0.1119 0.0785 -1.4251 1.54e-01 no rs1788002 53387425 C/T 0.3854 0.5444 0.0556 0.1137 0.4892 6.25e-01 no rs12969847 53388714 A/T 0.6410 0.2528 -0.1084 0.1290 -0.8404 4.01e-01 no rs8094527 53388926 C/T 0.6410 0.7389 0.1084 0.1290 0.8404 4.01e-01 no rs1736434 53388988 G/T 0.2437 0.0064 0.3532 0.7578 0.4661 6.41e-01 1.0000 rs2272783 53389818 C/T - 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