****** Results of the Case-control Association Tests ****** There are 1583 individuals from 141 independent families in the phenotype data file. Of these, 836 are affected, 190 are unaffected and 557 are of unknown phenotype. There are 1042 individuals listed in the genotype file, 1042 of whom are also in the phenotype file (excluding inbred individuals). The prevalence value used in the MIQLS calculations is 0.050000. The number of markers in each haplotype window is 2. ***************************************************** Analysis of SNP window rs1933024 rs2519016 ***************************************************** There are 906 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 726 are affected, 165 are unaffected and 15 are of unknown phenotype. Haplotype clusters in the full-df test cluster 1: G-C G-T A-C cluster 2: A-T Full-df MIQLS_b test Statistic = 0.493509 pvalue = 0.482366 df = 1 1-df MIQLS_b tests Haplotype tested Statistic P-value G-C 1.024190 0.311527 A-T 0.493509 0.482366 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.0064 0.0061 0.0030 0.0000 G-C 0.7995 0.8191 0.7721 0.8549 A-T 0.1859 0.1678 0.2109 0.1436 G-T 0.0082 0.0070 0.0140 0.0015 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.0047 0.0051 0.0034 0.0000 G-C 0.8127 0.8183 0.7878 0.8334 A-T 0.1760 0.1708 0.1978 0.1645 G-T 0.0066 0.0057 0.0110 0.0021 ***************************************************** Analysis of SNP window rs2519016 rs2980319 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 3.423998 pvalue = 0.330754 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value C-A 1.056145 0.304096 T-A 0.707300 0.400342 C-T 0.874904 0.349601 T-T 0.776724 0.378145 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.4353 0.4484 0.4185 0.4239 T-A 0.1206 0.1123 0.1423 0.1003 C-T 0.3742 0.3728 0.3716 0.4172 T-T 0.0699 0.0666 0.0676 0.0585 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.4493 0.4549 0.4201 0.4410 T-A 0.1170 0.1140 0.1357 0.1257 C-T 0.3575 0.3537 0.3781 0.3776 T-T 0.0762 0.0774 0.0661 0.0557 ***************************************************** Analysis of SNP window rs2980319 rs2799064 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Haplotype clusters in the full-df test cluster 1: A-G cluster 2: T-T cluster 3: T-G Full-df MIQLS_b test Statistic = 0.664566 pvalue = 0.717284 df = 2 1-df MIQLS_b tests Haplotype tested Statistic P-value A-G 0.517617 0.47186 T-G 0.345718 0.556547 T-T 0.182145 0.669536 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-G 0.5578 0.5693 0.5648 0.5243 T-G 0.0711 0.0630 0.0825 0.0667 T-T 0.3710 0.3677 0.3528 0.4090 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-G 0.5754 0.5774 0.5679 0.5667 T-G 0.0640 0.0599 0.0802 0.0667 T-T 0.3606 0.3627 0.3519 0.3667 ***************************************************** Analysis of SNP window rs2799064 rs3128126 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 3.145731 pvalue = 0.369697 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value G-A 0.146317 0.70208 T-A 0.897987 0.343322 G-G 0.634304 0.425781 T-G 1.482327 0.223411 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown G-A 0.1177 0.1167 0.1205 0.0389 T-A 0.0954 0.0988 0.0845 0.1123 G-G 0.5128 0.5213 0.5251 0.5300 T-G 0.2742 0.2632 0.2698 0.3189 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown G-A 0.1144 0.1148 0.1188 0.0521 T-A 0.0964 0.0984 0.0885 0.0897 G-G 0.5309 0.5299 0.5324 0.5538 T-G 0.2583 0.2570 0.2603 0.3044 ***************************************************** Analysis of SNP window rs3128126 rs9442372 ***************************************************** There are 903 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 722 are affected, 165 are unaffected and 16 are of unknown phenotype. Haplotype clusters in the full-df test cluster 1: G-G cluster 2: A-A Full-df MIQLS_b test Statistic = 0.474766 pvalue = 0.490802 df = 1 1-df MIQLS_b tests Haplotype tested Statistic P-value A-A 0.474766 0.490802 G-G 0.474766 0.490802 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.1958 0.2026 0.1888 0.1410 G-G 0.8042 0.7974 0.8112 0.8590 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.1905 0.1910 0.1942 0.1333 G-G 0.8095 0.8090 0.8058 0.8667 ***************************************************** Analysis of SNP window rs9442372 rs6701114 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 1.506413 pvalue = 0.680791 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value A-C 0.088729 0.765799 G-C 0.412256 0.520827 A-T 0.006218 0.937149 G-T 1.477248 0.224206 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.1657 0.1629 0.1942 0.0509 G-C 0.6016 0.6133 0.5960 0.6906 A-T 0.0479 0.0468 0.0369 0.0851 G-T 0.1848 0.1770 0.1728 0.1734 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.1707 0.1666 0.1992 0.0444 G-C 0.6104 0.6138 0.5913 0.6745 A-T 0.0432 0.0439 0.0380 0.0805 G-T 0.1757 0.1758 0.1715 0.2006 ***************************************************** Analysis of SNP window rs6701114 rs10907174 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 1.121765 pvalue = 0.771823 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value C-A 0.636056 0.425143 T-A 0.747933 0.387131 C-T 0.140940 0.707348 T-T 0.248692 0.617998 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.7446 0.7522 0.7707 0.7403 T-A 0.2205 0.2109 0.1974 0.2589 C-T 0.0243 0.0271 0.0195 0.0007 T-T 0.0106 0.0099 0.0125 0.0000 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.7553 0.7525 0.7718 0.7167 T-A 0.2102 0.2119 0.1948 0.2821 C-T 0.0259 0.0273 0.0213 0.0012 T-T 0.0086 0.0083 0.0120 0.0000 ***************************************************** Analysis of SNP window rs10907174 rs3813199 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 1.315294 pvalue = 0.725505 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value A-A 1.107615 0.292601 T-A 0.000026 0.995959 A-G 1.266170 0.260486 T-G 0.016897 0.896576 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.7195 0.7242 0.7157 0.7945 T-A 0.0235 0.0244 0.0270 0.0000 A-G 0.2458 0.2389 0.2505 0.2046 T-G 0.0112 0.0125 0.0068 0.0008 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.7239 0.7233 0.7202 0.7814 T-A 0.0241 0.0245 0.0251 0.0000 A-G 0.2410 0.2405 0.2456 0.2178 T-G 0.0110 0.0117 0.0090 0.0008 ***************************************************** Analysis of SNP window rs3813199 rs6603781 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 2.676220 pvalue = 0.444284 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value A-A 2.550823 0.110237 G-A 0.966045 0.325669 A-G 0.625836 0.428887 G-G 0.236320 0.626877 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.5498 0.5627 0.5374 0.7015 G-A 0.1891 0.1796 0.2020 0.1344 A-G 0.1937 0.1890 0.2063 0.0761 G-G 0.0674 0.0687 0.0544 0.0880 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.5590 0.5613 0.5385 0.6589 G-A 0.1823 0.1811 0.1927 0.1409 A-G 0.1883 0.1856 0.2084 0.1075 G-G 0.0704 0.0720 0.0604 0.0928 ***************************************************** Analysis of SNP window rs6603781 rs7515488 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 1.172822 pvalue = 0.75953 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value A-C 0.918895 0.337765 G-C 0.393030 0.530711 A-T 0.016535 0.897684 G-T 0.592834 0.441325 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.4621 0.4654 0.4396 0.4312 G-C 0.1909 0.1850 0.1914 0.1623 A-T 0.2742 0.2750 0.2991 0.4050 G-T 0.0728 0.0746 0.0700 0.0015 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.4624 0.4676 0.4426 0.4017 G-C 0.1872 0.1856 0.1972 0.1983 A-T 0.2785 0.2739 0.2903 0.3984 G-T 0.0719 0.0729 0.0699 0.0017 ***************************************************** Analysis of SNP window rs7515488 rs6603785 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 2.599640 pvalue = 0.457553 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value C-A 0.408978 0.522489 T-A 0.964304 0.326105 C-T 0.231666 0.630291 T-T 0.826711 0.363225 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.4504 0.4457 0.4659 0.2454 T-A 0.2299 0.2311 0.2461 0.3637 C-T 0.2008 0.2009 0.1671 0.3039 T-T 0.1189 0.1223 0.1209 0.0870 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.4593 0.4602 0.4732 0.2419 T-A 0.2322 0.2254 0.2515 0.3519 C-T 0.1861 0.1894 0.1634 0.3206 T-T 0.1225 0.1250 0.1119 0.0857 ***************************************************** Analysis of SNP window rs6603785 rs6603787 ***************************************************** There are 910 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 729 are affected, 165 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 1.566127 pvalue = 0.667094 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value A-G 0.168594 0.681365 T-G 1.474629 0.224617 A-T 0.484256 0.486501 T-T 0.087653 0.767183 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-G 0.0644 0.0675 0.0605 0.0439 T-G 0.1070 0.0975 0.1105 0.1261 A-T 0.6182 0.6185 0.6594 0.5939 T-T 0.2105 0.2165 0.1697 0.2360 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-G 0.0712 0.0733 0.0631 0.0518 T-G 0.0878 0.0830 0.1052 0.1309 A-T 0.6422 0.6362 0.6744 0.5761 T-T 0.1988 0.2076 0.1573 0.2412 ***************************************************** Analysis of SNP window rs6603787 rs7524470 ***************************************************** There are 910 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 729 are affected, 165 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 4.140156 pvalue = 0.246722 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value G-A 0.471501 0.492298 T-A 0.217371 0.641051 G-G 2.298752 0.129478 T-G 0.082378 0.7741 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown G-A 0.1475 0.1441 0.1445 0.2380 T-A 0.6858 0.6834 0.7177 0.6109 G-G 0.0215 0.0229 0.0220 0.0000 T-G 0.1453 0.1496 0.1159 0.1511 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown G-A 0.1417 0.1383 0.1495 0.2433 T-A 0.7048 0.7051 0.7068 0.6124 G-G 0.0182 0.0183 0.0190 0.0000 T-G 0.1354 0.1382 0.1246 0.1443 ***************************************************** Analysis of SNP window rs7524470 rs3753340 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 0.654501 pvalue = 0.88385 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value A-A 0.206292 0.649689 G-A 0.043109 0.83552 A-G 0.420882 0.516497 G-G 0.273333 0.601105 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.7311 0.7305 0.7843 0.7641 G-A 0.1380 0.1428 0.1170 0.0634 A-G 0.1006 0.0958 0.0801 0.1004 G-G 0.0303 0.0308 0.0186 0.0721 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.7545 0.7477 0.7807 0.7783 G-A 0.1290 0.1313 0.1254 0.0658 A-G 0.0895 0.0924 0.0766 0.0970 G-G 0.0270 0.0285 0.0173 0.0589 ***************************************************** Analysis of SNP window rs3753340 rs2296475 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 1.591230 pvalue = 0.66138 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value A-C 0.673570 0.41181 G-C 0.444639 0.504892 A-T 1.563221 0.211194 G-T 0.289195 0.590737 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.0737 0.0668 0.0777 0.0370 G-C 0.0674 0.0616 0.0592 0.0372 A-T 0.7963 0.8072 0.8254 0.7899 G-T 0.0626 0.0644 0.0378 0.1359 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.0661 0.0627 0.0829 0.0316 G-C 0.0553 0.0568 0.0523 0.0310 A-T 0.8189 0.8177 0.8250 0.8120 G-T 0.0597 0.0628 0.0398 0.1254 ***************************************************** Analysis of SNP window rs2296475 rs2296474 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 6.388565 pvalue = 0.0941623 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value C-A 0.546046 0.459938 T-A 3.802491 0.0511764 C-T 1.189004 0.275531 T-T 6.060513 0.0138238 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.0261 0.0209 0.0256 0.0372 T-A 0.1308 0.1241 0.1419 0.0574 C-T 0.1149 0.1067 0.1115 0.0371 T-T 0.7282 0.7483 0.7210 0.8684 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.0173 0.0161 0.0199 0.0314 T-A 0.1228 0.1192 0.1447 0.0625 C-T 0.1041 0.1032 0.1159 0.0312 T-T 0.7558 0.7614 0.7195 0.8750 ***************************************************** Analysis of SNP window rs2296474 rs6656541 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Haplotype clusters in the full-df test cluster 1: T-T cluster 2: T-G cluster 3: A-T Full-df MIQLS_b test Statistic = 3.233989 pvalue = 0.198494 df = 2 1-df MIQLS_b tests Haplotype tested Statistic P-value T-G 0.426509 0.513707 A-T 3.233980 0.0721252 T-T 0.452405 0.501195 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown T-G 0.4121 0.4226 0.3976 0.3090 A-T 0.1572 0.1470 0.1675 0.0944 T-T 0.4307 0.4304 0.4348 0.5966 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown T-G 0.4154 0.4247 0.3910 0.2812 A-T 0.1409 0.1351 0.1699 0.0937 T-T 0.4436 0.4402 0.4391 0.6250 ***************************************************** Analysis of SNP window rs6656541 rs7540231 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 1.990447 pvalue = 0.574392 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value G-A 0.097532 0.754812 T-A 1.955404 0.162006 G-G 0.297337 0.585557 T-G 0.338338 0.56079 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown G-A 0.1982 0.1967 0.2012 0.1803 T-A 0.2650 0.2538 0.2566 0.3106 G-G 0.2083 0.2229 0.1889 0.1111 T-G 0.3285 0.3266 0.3533 0.3980 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown G-A 0.2012 0.2022 0.2009 0.1715 T-A 0.2501 0.2464 0.2600 0.2893 G-G 0.2124 0.2201 0.1908 0.0950 T-G 0.3364 0.3312 0.3483 0.4442 ***************************************************** Analysis of SNP window rs7540231 rs16825288 ***************************************************** There are 911 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 729 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 1.060485 pvalue = 0.786621 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value A-A 0.466424 0.494637 G-A 0.216219 0.641936 A-G 0.238254 0.62547 G-G 0.568524 0.450846 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.3414 0.3406 0.3151 0.4170 G-A 0.4034 0.4131 0.4002 0.3685 A-G 0.1205 0.1122 0.1431 0.0671 G-G 0.1347 0.1340 0.1416 0.1474 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-A 0.3367 0.3399 0.3168 0.3840 G-A 0.4110 0.4160 0.3943 0.3825 A-G 0.1136 0.1074 0.1447 0.0693 G-G 0.1387 0.1367 0.1441 0.1643 ***************************************************** Analysis of SNP window rs16825288 rs6603811 ***************************************************** There are 911 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 729 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 4.740933 pvalue = 0.19178 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value A-C 0.300965 0.583278 G-C 0.005935 0.938594 A-T 0.587146 0.443525 G-T 4.581408 0.0323206 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.7200 0.7290 0.6836 0.7661 G-C 0.2464 0.2436 0.2694 0.1898 A-T 0.0244 0.0220 0.0306 0.0001 G-T 0.0092 0.0054 0.0164 0.0440 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-C 0.7192 0.7302 0.6721 0.7499 G-C 0.2514 0.2446 0.2816 0.2144 A-T 0.0230 0.0211 0.0304 0.0001 G-T 0.0064 0.0042 0.0158 0.0356 ***************************************************** Analysis of SNP window rs6603811 rs11260616 ***************************************************** There are 911 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 729 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 3.485855 pvalue = 0.322601 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value C-A 0.071769 0.788778 T-A 3.179337 0.074575 C-T 0.651199 0.419684 T-T 0.014738 0.903374 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.5582 0.5612 0.5379 0.5434 T-A 0.0240 0.0175 0.0372 0.0495 C-T 0.4084 0.4127 0.4182 0.4071 T-T 0.0094 0.0086 0.0067 0.0000 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown C-A 0.5483 0.5541 0.5201 0.5498 T-A 0.0203 0.0164 0.0370 0.0407 C-T 0.4238 0.4216 0.4371 0.4095 T-T 0.0077 0.0078 0.0058 0.0000 ***************************************************** Analysis of SNP window rs11260616 rs12126768 ***************************************************** There are 903 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 724 are affected, 163 are unaffected and 16 are of unknown phenotype. Haplotype clusters in the full-df test cluster 1: A-T cluster 2: T-T T-G cluster 3: A-G Full-df MIQLS_b test Statistic = 1.928547 pvalue = 0.38126 df = 2 1-df MIQLS_b tests Haplotype tested Statistic P-value A-G 0.009505 0.922334 A-T 1.526508 0.216637 T-T 1.807217 0.178842 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown A-G 0.0881 0.0892 0.0529 0.2029 T-G 0.0031 0.0038 0.0000 0.0000 A-T 0.4945 0.4872 0.5264 0.3986 T-T 0.4143 0.4197 0.4206 0.3985 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown A-G 0.0718 0.0727 0.0580 0.1819 T-G 0.0020 0.0024 0.0000 0.0000 A-T 0.5013 0.5004 0.5116 0.4094 T-T 0.4249 0.4246 0.4304 0.4087 ***************************************************** Analysis of SNP window rs12126768 rs6687065 ***************************************************** There are 912 individuals with genotype data for at least one SNP in the current haplotype window. Of these, 730 are affected, 166 are unaffected and 16 are of unknown phenotype. Full-df MIQLS_b test Statistic = 0.139860 pvalue = 0.986658 df = 3 1-df MIQLS_b tests Haplotype tested Statistic P-value G-A 0.051406 0.820635 T-A 0.012950 0.909398 G-G 0.006920 0.933705 T-G 0.116248 0.73314 Haplotype frequency estimates by phenotype category (IQL_b estimator) Haplotype Overall Affected Unaffected Unknown G-A 0.0632 0.0618 0.0470 0.2332 T-A 0.6487 0.6476 0.6577 0.3489 G-G 0.0192 0.0212 0.0163 0.0000 T-G 0.2689 0.2693 0.2790 0.4179 Haplotype frequency estimates by phenotype category (EW_b estimator) Haplotype Overall Affected Unaffected Unknown G-A 0.0576 0.0550 0.0611 0.2148 T-A 0.6512 0.6537 0.6591 0.3551 G-G 0.0165 0.0172 0.0159 0.0000 T-G 0.2747 0.2741 0.2638 0.4301