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LD-PAC Web Server Results


This is the result of WTCCC T2D whole genome data including all QC-excluded (spurious) associations. Our method effectively detects many spurious associations (red dots). Running this example takes only 10 minutes. Click on each SNP RSID for details.



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Input Output
RSID Chr Position P-value LD-PAC Prediction LD-PAC Statistic
(Log Likelihood ratio, LR)
rs1022579 1 17311782 6.94E-12 SPURIOUS +5.07
rs12744552 1 84989273 1.62E-17 SPURIOUS +6.77
rs1413235 1 97458624 9.06E-39 SPURIOUS +29.79
rs11166411 1 100417088 1.98E-65 SPURIOUS +34.85
rs17353053 1 144972536 3.44E-10 SPURIOUS +5.81
rs2999538 1 150251582 2.18E-29 SPURIOUS +12.74
rs853747 1 212111680 1.67E-08 SPURIOUS +3.03
rs1640803 1 221400672 4.02E-11 AMBIGUOUS +1.98
rs12043362 1 236027581 5.72E-09 AMBIGUOUS +1.02
rs6422705 2 4953828 7.39E-08 AMBIGUOUS +2.33
rs902133 2 10875636 9.70E-12 SPURIOUS +6.12
rs10184046 2 39190207 1.11E-49 SPURIOUS +32.39
rs7591885 2 45887102 5.44E-10 AMBIGUOUS +2.28
rs1377233 2 50182138 6.41E-24 SPURIOUS +12.31
rs1502598 2 82778693 7.61E-11 SPURIOUS +6.08
rs1437741 2 85822090 3.65E-07 AMBIGUOUS +0.96
rs6735537 2 88092105 2.81E-14 UNTESTED
rs1349743 2 117768082 6.18E-10 SPURIOUS +3.56
rs10171121 2 150551330 4.44E-14 SPURIOUS +9.64
rs10185950 2 151033549 3.74E-10 SPURIOUS +5.59
rs582397 2 156972295 5.33E-107 SPURIOUS +81.23
rs6712841 2 174021646 2.15E-07 AMBIGUOUS +1.53
rs17667540 2 181323158 1.78E-26 SPURIOUS +14.07
rs7596121 2 196355134 9.80E-47 SPURIOUS +34.02
rs7572953 2 197194201 3.31E-159 SPURIOUS +111.22
rs7653834 3 17026332 1.14E-27 SPURIOUS +14.29
rs753820 3 58589443 8.27E-09 AMBIGUOUS +2.08
rs17060743 3 59420738 6.57E-15 SPURIOUS +7.86
rs9845503 3 59676017 2.44E-07 SPURIOUS +4.21
rs1378850 3 67066723 4.57E-177 SPURIOUS +144.27
rs13064754 3 80399557 4.42E-11 SPURIOUS +5.06
rs2862073 3 154706312 4.86E-10 SPURIOUS +4.61
rs2101167 3 158174102 9.25E-14 SPURIOUS +8.97
rs6449197 4 15424020 1.37E-07 SPURIOUS +3.10
rs11466651 4 38452715 6.73E-16 SPURIOUS +8.36
rs17027888 4 99790237 1.29E-11 UNTESTED
rs17669915 4 109431209 8.93E-09 AMBIGUOUS +1.73
rs893023 4 148971809 7.11E-19 SPURIOUS +8.82
rs583835 5 3926124 1.69E-08 AMBIGUOUS +2.02
rs3804263 5 54771543 1.50E-08 AMBIGUOUS +0.73
rs16877062 5 79034659 9.20E-10 SPURIOUS +3.07
rs9326985 5 115453102 1.48E-84 SPURIOUS +67.35
rs17053134 5 155373544 5.67E-12 SPURIOUS +6.94
rs10045570 5 159193718 8.91E-59 SPURIOUS +43.03
rs17067598 5 166166487 1.08E-09 SPURIOUS +3.56
rs9396603 6 9914862 5.43E-12 SPURIOUS +5.49
rs9295736 6 11088294 9.86E-41 SPURIOUS +31.12
rs16880603 6 18469264 4.02E-07 AMBIGUOUS +0.22
rs29233 6 29719208 7.67E-13 SPURIOUS +8.60
rs9462616 6 40464159 4.26E-09 AMBIGUOUS +1.98
rs6929834 6 42816606 1.87E-27 SPURIOUS +11.45
rs539002 6 44891615 2.86E-09 AMBIGUOUS -0.72
rs3777582 6 46022006 9.97E-31 SPURIOUS +18.77
rs1324132 6 93805420 2.28E-07 SPURIOUS +3.68
rs9402228 6 99426305 1.26E-13 SPURIOUS +8.20
rs10499044 6 107247988 4.43E-21 UNTESTED
rs17077879 6 148374751 9.60E-15 UNTESTED
rs9478918 6 151399992 4.75E-08 AMBIGUOUS +2.43
rs3006172 6 169637287 2.32E-15 SPURIOUS +5.89
rs1494192 7 24153338 1.43E-23 SPURIOUS +11.66
rs11771762 7 25211954 2.28E-08 AMBIGUOUS +0.71
rs7801967 7 28211820 3.76E-17 SPURIOUS +8.14
rs6971267 7 37109212 1.60E-07 SPURIOUS +3.57
rs17171848 7 41343772 1.16E-13 SPURIOUS +3.49
rs1477523 7 136455678 2.10E-08 SPURIOUS +4.41
rs17076408 8 2586038 2.82E-13 SPURIOUS +5.87
rs4602914 8 3345841 1.34E-24 SPURIOUS +9.43
rs17075115 8 5758247 1.98E-16 AMBIGUOUS +2.67
rs17480050 8 19426197 1.00E-100 SPURIOUS +43.79
rs6474409 8 42609235 4.96E-07 AMBIGUOUS +0.15
rs10975953 9 6986621 8.71E-10 AMBIGUOUS +2.56
rs16930665 9 13660365 1.30E-07 AMBIGUOUS +2.27
rs11142822 9 73232063 7.77E-09 SPURIOUS +6.08
rs4402212 10 57666390 3.30E-08 SPURIOUS +6.41
rs2014327 10 61184008 2.57E-08 UNTESTED
rs10996819 10 67429012 6.22E-09 AMBIGUOUS +2.09
rs490265 10 89951510 7.99E-23 SPURIOUS +10.83
rs17110738 10 97167744 1.43E-07 SPURIOUS +4.03
rs7917983 10 114722872 6.72E-08 TRUE -8.05
rs7901275 10 114722896 3.87E-08 TRUE -7.57
rs4074720 10 114738487 6.02E-11 TRUE -10.06
rs7901695 10 114744078 9.80E-13 TRUE -10.64
rs4506565 10 114746031 8.01E-13 TRUE -11.49
rs4132670 10 114757761 2.68E-12 TRUE -10.91
rs10787472 10 114771287 2.56E-11 TRUE -11.67
rs12243326 10 114778805 1.92E-10 TRUE -9.18
rs11196205 10 114797037 8.12E-11 TRUE -10.45
rs10885409 10 114798062 9.72E-11 TRUE -8.85
rs11196208 10 114801306 6.37E-11 TRUE -9.63
rs3758589 10 115301037 2.11E-07 AMBIGUOUS +0.29
rs2944490 10 132901716 1.61E-12 SPURIOUS +8.94
rs11042656 11 10171031 1.18E-26 SPURIOUS +14.40
rs4939179 11 57603286 3.96E-08 SPURIOUS +3.66
rs17833579 11 87203798 4.20E-08 AMBIGUOUS +2.98
rs10501796 11 92092804 3.39E-07 AMBIGUOUS +0.97
rs10771596 12 9412754 6.80E-09 UNTESTED
rs10505911 12 23913427 1.57E-07 AMBIGUOUS +0.75
rs285584 12 40232806 3.98E-07 AMBIGUOUS +2.15
rs1554428 12 41509821 4.80E-10 SPURIOUS +4.66
rs17102640 12 52442003 7.50E-45 UNTESTED
rs10492267 12 96873469 1.14E-24 SPURIOUS +6.57
rs2052424 12 107468359 1.34E-07 AMBIGUOUS +2.50
rs7966820 12 108786653 9.16E-197 SPURIOUS +114.94
rs4379926 13 22064570 1.33E-07 AMBIGUOUS +2.73
rs3095526 13 50131567 6.38E-10 SPURIOUS +4.52
rs7987755 13 71626382 6.58E-11 SPURIOUS +5.16
rs1884094 14 60086686 1.36E-07 SPURIOUS +5.57
rs7149905 14 66569469 2.27E-21 SPURIOUS +13.28
rs7168730 15 36755514 4.65E-14 UNTESTED
rs352483 15 63615394 2.80E-28 SPURIOUS +17.42
rs11072089 15 67437107 7.01E-08 AMBIGUOUS +2.64
rs1871229 15 71801705 6.56E-11 SPURIOUS +4.56
rs3093412 16 27369022 2.01E-08 UNTESTED
rs2919427 16 30576592 4.33E-08 UNTESTED
rs36469 16 45337768 1.34E-51 SPURIOUS +29.28
rs9939973 16 52358069 2.93E-07 TRUE -5.94
rs9940128 16 52358255 3.06E-07 TRUE -7.71
rs1121980 16 52366748 3.30E-07 TRUE -4.22
rs7193144 16 52368187 1.88E-08 TRUE -5.58
rs8050136 16 52373776 2.47E-08 TRUE -7.78
rs17843021 17 36370254 3.27E-08 SPURIOUS +5.35
rs13380910 18 8466957 4.55E-08 UNTESTED
rs370233 18 11311282 1.99E-53 SPURIOUS +32.93
rs4801109 18 50722432 9.85E-24 SPURIOUS +10.76
rs1513587 20 11678088 1.03E-10 SPURIOUS +4.48
rs11705626 22 23765959 5.34E-80 SPURIOUS +53.18
rs7292491 22 24525440 6.63E-10 SPURIOUS +4.16
rs6518796 22 31511302 5.86E-98 SPURIOUS +53.50

SPURIOUS: LR > +3.0
TRUE: LR < -3.0
AMBIGUOUS: -3.0 < LR < +3.0
UNTESTED: Untested because the SNP has too few (< 3) neighboring markers (r2>0.1) in LD

The associations below were not tested because the SNPs are not included or not polymorphic in the HapMap data we used.

RSIDP-value
rs4557934 1.30E-19
rs4418594 8.93E-10
rs2153676 5.41E-11
rs863111 8.09E-18
rs16840119 4.45E-46
rs16848754 3.61E-13
rs851148 3.99E-07
rs10193882 5.91E-08
rs1522103 1.33E-16
rs3739128 6.53E-16
rs12469530 3.15E-92
rs4675440 2.62E-12
rs7568886 5.32E-08
rs7644124 4.20E-07
rs16837871 6.08E-24
rs1444360 2.64E-10
rs940575 8.00E-08
rs7666328 6.89E-08
rs1490855 2.28E-07
rs4512120 6.41E-13
rs16876548 5.88E-21
rs2416472 2.51E-16
rs10498719 2.89E-19
rs1110235 3.61E-11
rs12198616 9.97E-173
rs11756328 1.03E-11
rs4947143 7.07E-316
rs195519 1.51E-27
rs9385758 4.55E-07
rs9385815 3.70E-11
rs13241710 2.17E-07
rs4541810 1.19E-07
rs10237977 4.31E-07
rs7015044 4.62E-46
rs2259576 5.76E-12
rs1380104 2.98E-13
rs1830189 3.45E-32
rs10103486 1.82E-13
rs1521822 3.51E-11
rs2511675 1.82E-12
rs16870588 6.19E-10
rs7849137 2.25E-10
rs2891142 8.86E-61
rs7047811 1.14E-22
rs17176454 5.35E-08
rs3780786 6.91E-08
rs4526685 1.75E-12
rs1398025 5.73E-55
rs1763398 1.25E-08
rs657293 3.14E-07
rs11597556 4.06E-12
rs7901263 3.37E-147
rs7070288 7.72E-09
rs7090761 1.50E-10
rs7899146 6.16E-38
rs17232271 1.54E-07
rs7069226 1.73E-07
rs7077039 3.79E-12
rs17155289 3.91E-07
rs2433469 5.61E-10
rs11038203 2.74E-07
rs10894818 3.63E-07
rs17835004 5.69E-14
rs9668009 2.11E-11
rs17029313 1.97E-07
rs1532723 1.14E-07
rs7976158 1.92E-13
rs7338329 3.49E-07
rs9587093 1.19E-08
rs1536053 2.37E-10
rs2792111 7.83E-09
rs17434055 8.21E-20
rs915372 6.58E-08
rs2278316 1.43E-13
rs168389 4.50E-07
rs10851802 1.47E-08
rs12325390 7.74E-13
rs9939609 6.43E-08
rs12923504 1.26E-08
rs2688025 3.84E-16
rs4129589 6.28E-08
rs3810054 5.08E-57
rs16967980 2.53E-11
rs1424508 1.33E-16
rs3973371 4.12E-08
rs6027756 1.51E-20
rs2775017 5.02E-08
rs226261 6.06E-08
rs8139244 1.42E-35