******Results of the Case-control Association tests ****** There are 2420 individuals from 620 independent families. 700 of the individuals are affected, 1720 of the individuals are unaffected, and 0 of the individuals are of unknown phenotype. There are 1210 males and 1210 females. The prevalence values used in the MQLS test statistic for males and females are 0.085625 and 0.085652, respectively. **************************************** Analysis of Marker 1: rs3094315 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 30.696586 pvalue = 3.01695e-08 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -155.2143) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 19.957045 pvalue = 7.92016e-06 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 14.728657 pvalue = 0.000124145 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -82.8633) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3681 sd = 0.0200 freq = 0.4731 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4400 sd = 0.0125 allele 2 : freq = 0.6319 sd = 0.0200 freq = 0.5269 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5600 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3553 freq = 0.4648 freq = 0.0000 freq = 0.4240 allele 2 : freq = 0.6447 freq = 0.5352 freq = 0.0000 freq = 0.5760 ***************************************** **************************************** Analysis of Marker 2: rs2286139 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 53.212433 pvalue = 2.99358e-13 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -204.2962) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 33.524379 pvalue = 7.03763e-09 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 26.761652 pvalue = 2.3016e-07 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -111.6617) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3224 sd = 0.0194 freq = 0.4715 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4268 sd = 0.0124 allele 2 : freq = 0.6776 sd = 0.0194 freq = 0.5285 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5732 sd = 0.0124 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3197 freq = 0.4617 freq = 0.0000 freq = 0.4088 allele 2 : freq = 0.6803 freq = 0.5383 freq = 0.0000 freq = 0.5912 ***************************************** **************************************** Analysis of Marker 3: rs11240776 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 17.295837 pvalue = 3.19887e-05 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -117.0316) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 7.813402 pvalue = 0.00518602 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 11.278069 pvalue = 0.000784281 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -72.8356) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3931 sd = 0.0203 freq = 0.4648 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4393 sd = 0.0125 allele 2 : freq = 0.6069 sd = 0.0203 freq = 0.5352 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5607 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3882 freq = 0.4570 freq = 0.0000 freq = 0.4314 allele 2 : freq = 0.6118 freq = 0.5430 freq = 0.0000 freq = 0.5686 ***************************************** **************************************** Analysis of Marker 4: rs2980300 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 52.939498 pvalue = 3.43982e-13 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -205.9799) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 33.689399 pvalue = 6.46521e-09 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 27.654383 pvalue = 1.45043e-07 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -114.7390) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3517 sd = 0.0198 freq = 0.4929 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4512 sd = 0.0125 allele 2 : freq = 0.6483 sd = 0.0198 freq = 0.5071 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5488 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3382 freq = 0.4820 freq = 0.0000 freq = 0.4284 allele 2 : freq = 0.6618 freq = 0.5180 freq = 0.0000 freq = 0.5716 ***************************************** **************************************** Analysis of Marker 5: rs2905036 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 47.631157 pvalue = 5.14443e-12 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -192.1657) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 43.354500 pvalue = 4.56685e-11 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 44.815015 pvalue = 2.16556e-11 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -143.6601) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3457 sd = 0.0197 freq = 0.5013 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4518 sd = 0.0125 allele 2 : freq = 0.6543 sd = 0.0197 freq = 0.4987 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5482 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3395 freq = 0.5000 freq = 0.0000 freq = 0.4402 allele 2 : freq = 0.6605 freq = 0.5000 freq = 0.0000 freq = 0.5598 ***************************************** **************************************** Analysis of Marker 6: rs4245756 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 29.095521 pvalue = 6.88961e-08 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -149.8983) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 17.225221 pvalue = 3.31999e-05 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 18.765209 pvalue = 1.4784e-05 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -92.7800) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3862 sd = 0.0202 freq = 0.4897 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4555 sd = 0.0125 allele 2 : freq = 0.6138 sd = 0.0202 freq = 0.5103 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5445 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3803 freq = 0.4813 freq = 0.0000 freq = 0.4436 allele 2 : freq = 0.6197 freq = 0.5188 freq = 0.0000 freq = 0.5564 ***************************************** **************************************** Analysis of Marker 7: rs3748597 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 26.244437 pvalue = 3.0082e-07 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -147.4626) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 19.836909 pvalue = 8.43383e-06 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 19.645889 pvalue = 9.32036e-06 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -98.3316) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3534 sd = 0.0198 freq = 0.4706 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4336 sd = 0.0124 allele 2 : freq = 0.6466 sd = 0.0198 freq = 0.5294 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5664 sd = 0.0124 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3487 freq = 0.4609 freq = 0.0000 freq = 0.4191 allele 2 : freq = 0.6513 freq = 0.5391 freq = 0.0000 freq = 0.5809 ***************************************** **************************************** Analysis of Marker 8: rs2341354 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 21.860417 pvalue = 2.9322e-06 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -130.3311) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 13.512840 pvalue = 0.000236937 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 11.681723 pvalue = 0.00063117 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -73.4288) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3914 sd = 0.0203 freq = 0.4843 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4554 sd = 0.0125 allele 2 : freq = 0.6086 sd = 0.0203 freq = 0.5157 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5446 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3868 freq = 0.4766 freq = 0.0000 freq = 0.4431 allele 2 : freq = 0.6132 freq = 0.5234 freq = 0.0000 freq = 0.5569 ***************************************** **************************************** Analysis of Marker 9: rs2465126 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 13.609092 pvalue = 0.000225093 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -102.1750) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 12.413834 pvalue = 0.000426165 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 7.881026 pvalue = 0.00499561 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -59.9260) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3888 sd = 0.0202 freq = 0.4577 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4358 sd = 0.0125 allele 2 : freq = 0.6112 sd = 0.0202 freq = 0.5423 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5642 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3724 freq = 0.4578 freq = 0.0000 freq = 0.4260 allele 2 : freq = 0.6276 freq = 0.5422 freq = 0.0000 freq = 0.5740 ***************************************** **************************************** Analysis of Marker 10: rs2465136 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 31.025999 pvalue = 2.54595e-08 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -161.8363) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 26.368388 pvalue = 2.8212e-07 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 17.098038 pvalue = 3.5499e-05 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -92.5934) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3690 sd = 0.0200 freq = 0.4955 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4557 sd = 0.0125 allele 2 : freq = 0.6310 sd = 0.0200 freq = 0.5045 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5443 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3592 freq = 0.4898 freq = 0.0000 freq = 0.4412 allele 2 : freq = 0.6408 freq = 0.5102 freq = 0.0000 freq = 0.5588 ***************************************** **************************************** Analysis of Marker 11: rs13129 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 31.840853 pvalue = 1.67336e-08 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -158.6755) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 20.031324 pvalue = 7.61839e-06 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 17.033386 pvalue = 3.67283e-05 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -89.4462) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3612 sd = 0.0199 freq = 0.4629 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4315 sd = 0.0124 allele 2 : freq = 0.6388 sd = 0.0199 freq = 0.5371 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5685 sd = 0.0124 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3461 freq = 0.4562 freq = 0.0000 freq = 0.4152 allele 2 : freq = 0.6539 freq = 0.5437 freq = 0.0000 freq = 0.5848 ***************************************** **************************************** Analysis of Marker 12: rs4075116 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 12.624241 pvalue = 0.000380776 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -99.5583) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 12.434164 pvalue = 0.000421551 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 7.327930 pvalue = 0.00678912 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -58.4601) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3888 sd = 0.0202 freq = 0.4600 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4384 sd = 0.0125 allele 2 : freq = 0.6112 sd = 0.0202 freq = 0.5400 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5616 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3697 freq = 0.4562 freq = 0.0000 freq = 0.4240 allele 2 : freq = 0.6303 freq = 0.5437 freq = 0.0000 freq = 0.5760 ***************************************** **************************************** Analysis of Marker 13: rs6667248 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 32.090533 pvalue = 1.47153e-08 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -156.2393) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 22.826902 pvalue = 1.77267e-06 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 22.369091 pvalue = 2.24966e-06 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -100.5356) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3526 sd = 0.0198 freq = 0.4708 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4307 sd = 0.0124 allele 2 : freq = 0.6474 sd = 0.0198 freq = 0.5292 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5693 sd = 0.0124 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3487 freq = 0.4641 freq = 0.0000 freq = 0.4211 allele 2 : freq = 0.6513 freq = 0.5359 freq = 0.0000 freq = 0.5789 ***************************************** **************************************** Analysis of Marker 14: rs9442372 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 37.767260 pvalue = 7.97084e-10 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -169.2952) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 22.718287 pvalue = 1.87574e-06 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 19.105315 pvalue = 1.237e-05 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -92.8022) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3724 sd = 0.0201 freq = 0.4842 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4460 sd = 0.0125 allele 2 : freq = 0.6276 sd = 0.0201 freq = 0.5158 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5540 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3632 freq = 0.4781 freq = 0.0000 freq = 0.4353 allele 2 : freq = 0.6368 freq = 0.5219 freq = 0.0000 freq = 0.5647 ***************************************** **************************************** Analysis of Marker 15: rs11260595 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 19.898526 pvalue = 8.16633e-06 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -122.2883) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 11.009946 pvalue = 0.000906243 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 8.263952 pvalue = 0.004044 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -60.7383) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3940 sd = 0.0203 freq = 0.4665 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4442 sd = 0.0125 allele 2 : freq = 0.6060 sd = 0.0203 freq = 0.5335 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5558 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3789 freq = 0.4586 freq = 0.0000 freq = 0.4289 allele 2 : freq = 0.6211 freq = 0.5414 freq = 0.0000 freq = 0.5711 ***************************************** **************************************** Analysis of Marker 16: rs6604968 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 29.582015 pvalue = 5.36e-08 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -152.1013) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 24.341125 pvalue = 8.06977e-07 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 20.056592 pvalue = 7.51839e-06 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -96.5254) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3569 sd = 0.0199 freq = 0.4738 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4372 sd = 0.0125 allele 2 : freq = 0.6431 sd = 0.0199 freq = 0.5262 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5628 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3526 freq = 0.4734 freq = 0.0000 freq = 0.4284 allele 2 : freq = 0.6474 freq = 0.5266 freq = 0.0000 freq = 0.5716 ***************************************** **************************************** Analysis of Marker 17: rs6686003 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 24.209067 pvalue = 8.64245e-07 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -135.6010) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 15.239749 pvalue = 9.46893e-05 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 12.909631 pvalue = 0.000326896 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -76.3176) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3638 sd = 0.0200 freq = 0.4603 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4286 sd = 0.0124 allele 2 : freq = 0.6362 sd = 0.0200 freq = 0.5397 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5714 sd = 0.0124 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3566 freq = 0.4508 freq = 0.0000 freq = 0.4157 allele 2 : freq = 0.6434 freq = 0.5492 freq = 0.0000 freq = 0.5843 ***************************************** **************************************** Analysis of Marker 18: rs9442385 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 13.313469 pvalue = 0.000263506 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -100.4008) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 15.287707 pvalue = 9.23153e-05 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 8.879469 pvalue = 0.00288395 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -63.1945) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3845 sd = 0.0202 freq = 0.4773 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4485 sd = 0.0125 allele 2 : freq = 0.6155 sd = 0.0202 freq = 0.5227 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5515 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3816 freq = 0.4758 freq = 0.0000 freq = 0.4407 allele 2 : freq = 0.6184 freq = 0.5242 freq = 0.0000 freq = 0.5593 ***************************************** **************************************** Analysis of Marker 19: rs11260554 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 59.388547 pvalue = 1.2942e-14 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -217.5958) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 60.870588 pvalue = 6.09527e-15 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 56.753136 pvalue = 4.94102e-14 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -163.9413) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3216 sd = 0.0194 freq = 0.5014 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4408 sd = 0.0125 allele 2 : freq = 0.6784 sd = 0.0194 freq = 0.4986 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5592 sd = 0.0125 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3079 freq = 0.5008 freq = 0.0000 freq = 0.4289 allele 2 : freq = 0.6921 freq = 0.4992 freq = 0.0000 freq = 0.5711 ***************************************** **************************************** Analysis of Marker 20: rs10907175 **************************************** There are 380 affected individuals, 640 unaffected individuals, and 0 individuals of unknown phenotype available. ***************************************** MQLS test using robust variance estimator MQLS statistic value = 49.684153 pvalue = 1.80599e-12 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -202.5954) ***************************************** Corrected chi-squared test using robust variance estimator Corrected chi-squared statistic value = 41.356513 pvalue = 1.26848e-10 df = 1 ***************************************** WQLS test using robust variance estimator WQLS statistic value = 39.784415 pvalue = 2.83599e-10 df = 1 Frequency of allele 1 is increased in the controls (quasi-score associated to this allele is -139.7241) ***************************************** allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3267 sd = 0.0195 freq = 0.4772 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.4300 sd = 0.0124 allele 2 : freq = 0.6733 sd = 0.0195 freq = 0.5228 sd = 0.0150 freq = 0.0000 sd = 0.0000 freq = 0.5700 sd = 0.0124 ***************************************** allele frequency estimates using naive counting in cases unaffected controls unknown controls all sample allele 1 : freq = 0.3132 freq = 0.4750 freq = 0.0000 freq = 0.4147 allele 2 : freq = 0.6868 freq = 0.5250 freq = 0.0000 freq = 0.5853 *****************************************