Skip to main content

Advertisement

Table 2 Epigenome-wide significant CpG sites for tobacco smoking in a veteran HIV-positive population: a meta-analysis

From: Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality

Probe Chr Position Nearest gene p dis Effect (SE)dis p rep Effect (SE)rep Z score p meta Direction Hat p
cg05575921 5 373,378 AHRR 3.64E−40 − 0.134 (0.009) 1.36E−40 − 0.164 (0.011) − 18.800 7.56E−79 0.480
cg21566642 2 233,284,661   1.35E−27 − 0.078 (0.007) 2.64E−36 − 0.096 (0.007) − 16.543 1.81E−61 0.076
cg01940273 2 233,284,934   1.53E−26 − 0.056 (0.005) 6.92E−33 − 0.068 (0.005) − 15.944 3.12E−57 0.144
cg23576855 5 373,299 AHRR 9.77E−31 − 0.117 (0.009) 3.67E−27 − 0.127 (0.011) − 15.791 3.58E−56 0.975
cg26703534 5 377,358 AHRR 4.18E−21 − 0.034 (0.003) 2.50E−17 − 0.038 (0.004) − 12.670 8.65E−37 0.811
cg21161138 5 399,360 AHRR 5.82E−18 − 0.034 (0.004) 8.62E−16 − 0.039 (0.005) − 11.803 3.78E−32 0.994
cg09935388 1 92,947,588 GFI1 1.47E−13 − 0.059 (0.008) 1.61E−18 − 0.090 (0.010) − 11.394 4.48E−30 0.167
cg03636183 19 17,000,585 F2RL3 2.42E−17 − 0.067 (0.008) 7.86E−12 − 0.056 (0.008) − 10.861 1.76E−27 0.438
cg21322436 7 145,812,842 CNTNAP2 9.60E−14 − 0.024 (0.003) 6.16E−15 − 0.028 (0.003) − 10.766 4.98E−27 0.532
cg03329539 2 233,283,329   1.29E−15 − 0.029 (0.003) 3.22E−12 − 0.030 (0.004) − 10.600 3.00E−26 0.720
cg25648203 5 395,444 AHRR 7.14E−13 − 0.025 (0.003) 2.29E−13 − 0.033 (0.004) − 10.248 1.20E−24 0.642
cg11660018 11 86,510,915 PRSS23 8.89E−11 − 0.024 (0.004) 1.02E−15 − 0.036 (0.004) − 10.215 1.69E−24 0.148
cg23771366 11 86,510,998 PRSS23 4.21E−07 − 0.020 (0.004) 4.97E−20 − 0.042 (0.004) − 9.951 2.50E−23 0.001
cg05284742 14 93,552,128 ITPK1 1.24E−13 − 0.018 (0.002) 3.22E−11 − 0.020 (0.003) − 9.947 2.60E−23 0.839
cg19572487 17 38,476,024 RARA 1.82E−08 − 0.024 (0.004) 3.79E−17 − 0.040 (0.005) − 9.858 6.30E−23 0.020
cg01901332 11 75,031,054 ARRB1 1.16E−14 − 0.031 (0.004) 8.50E−10 − 0.030 (0.005) − 9.830 8.32E−23 0.436
cg24859433 6 30,720,203   4.20E−11 − 0.024 (0.004) 3.64E−13 − 0.032 (0.004) − 9.782 1.35E−22 0.415
cg15342087 6 30,720,209   4.85E−11 − 0.023 (0.003) 6.14E−13 − 0.027 (0.004) − 9.718 2.54E−22 0.437
cg03450842 10 80,834,947 ZMIZ1 6.08E−11 − 0.018 (0.003) 5.02E−13 − 0.026 (0.003) − 9.712 2.69E−22 0.412
cg04551776 5 393,366 AHRR 7.00E−10 − 0.017 (0.003) 1.34E−13 − 0.029 (0.004) − 9.558 1.20E−21 0.227
cg12803068 7 45,002,919 MYO1G 8.63E−10 0.047 (0.008) 5.40E−12 0.064 (0.009) 9.188 4.02E−20 ++ 0.391
cg15212295 17 64,710,687 PRKCA 6.36E−10 − 0.014 (0.002) 1.22E−10 − 0.021 (0.003) − 8.911 5.07E−19 0.624
cg14753356 6 30,720,108   4.55E−09 − 0.018 (0.003) 6.42E−11 − 0.028 (0.004) − 8.744 2.25E−18 0.436
cg25189904 1 68,299,493 GNG12 3.14E−06 − 0.035 (0.008) 7.95E−15 − 0.066 (0.008) − 8.708 3.11E−18 0.012
cg02657160 3 98,311,063 CPOX 8.20E−10 − 0.014 (0.002) 7.79E−10 − 0.015 (0.002) − 8.685 3.79E−18 0.758
cg13193840 2 233,285,289   1.62E−08 − 0.013 (0.002) 4.55E−11 − 0.021 (0.003) − 8.622 6.58E−18 0.336
cg07986378 12 11,898,284 ETV6 1.54E−06 − 0.024 (0.005) 5.41E−13 − 0.040 (0.005) − 8.435 3.30E−17 0.046
cg22851561 14 74,214,183 C14orf43 5.28E−10 − 0.019 (0.003) 1.17E−08 − 0.026 (0.004) − 8.432 3.39E−17 0.948
cg27537125 1 25,349,681   1.45E−09 − 0.009 (0.002) 2.48E−08 − 0.010 (0.002) − 8.226 1.93E−16 0.960
cg06644428 2 233,284,112   2.07E−06 − 0.016 (0.003) 8.58E−12 − 0.029 (0.004) − 8.129 4.34E−16 0.079
cg14624207 11 68,142,198 LRP5 4.95E−09 − 0.015 (0.003) 2.13E−08 − 0.019 (0.003) − 8.098 5.61E−16 0.915
cg26271591 2 178,125,956 NFE2L2 5.49E−06 − 0.025 (0.005) 3.90E−12 − 0.052 (0.007) − 8.058 7.76E−16 0.048
cg11902777 5 368,843 AHRR 3.87E−10 − 0.012 (0.002) 5.52E−07 − 0.008 (0.002) − 7.993 1.32E−15 0.543
cg19859270 3 98,251,294 GPR15 2.46E−10 − 0.013 (0.002) 1.21E−06 − 0.007 (0.001) − 7.939 2.03E−15 0.443
cg08709672 1 206,224,334 AVPR1B 9.81E−09 − 0.021 (0.004) 8.12E−08 − 0.019 (0.004) − 7.852 4.09E−15 0.991
cg23916896 5 368,804 AHRR 1.14E−11 − 0.040 (0.006) 2.89E−05 − 0.019 (0.004) − 7.816 5.45E−15 0.116
cg19089201 7 45,002,287 MYO1G 7.39E−08 0.027 (0.005) 2.09E−08 0.042 (0.007) 7.758 8.63E−15 ++ 0.669
cg02583484 12 54,677,008 HNRNPA1 2.94E−06 − 0.013 (0.003) 3.50E−10 − 0.023 (0.004) − 7.699 1.37E−14 0.162
cg09022230 7 5,457,225 TNRC18 1.45E−07 − 0.019 (0.004) 2.52E−08 − 0.027 (0.005) − 7.646 2.07E−14 0.626
cg07178945 12 4,488,800 FGF23 1.87E−07 0.020 (0.004) 2.08E−08 0.028 (0.005) 7.635 2.27E−14 ++ 0.587
cg04885881 1 11,123,118   1.46E−06 − 0.025 (0.005) 1.79E−09 − 0.034 (0.006) − 7.626 2.43E−14 0.265
cg25949550 7 145,814,306 CNTNAP2 1.21E−08 − 0.011 (0.002) 4.80E−07 − 0.013 (0.002) − 7.601 2.94E−14 0.837
cg00073090 19 1,265,879   1.20E−05 − 0.011 (0.002) 1.97E−10 − 0.017 (0.003) − 7.542 4.63E−14 0.095
cg27241845 2 233,250,370   2.53E−06 − 0.019 (0.004) 1.98E−08 − 0.034 (0.006) − 7.270 3.59E−13 0.371
cg18900812 6 36,646,127 CDKN1A 4.74E−06 − 0.017 (0.004) 9.22E−09 − 0.021 (0.004) − 7.265 3.74E−13 0.280
cg15159987 19 17,003,890 CPAMD8 8.33E−10 − 0.019 (0.003) 1.11E−04 − 0.014 (0.004) − 7.125 1.04E−12 0.174
cg19254163 11 60,623,782 GPR44 6.38E−07 − 0.012 (0.002) 1.02E−06 − 0.019 (0.004) − 6.975 3.06E−12 0.859
cg08149865 8 21,914,600 EPB49 1.23E−06 − 0.014 (0.003) 9.45E−07 − 0.016 (0.003) − 6.891 5.53E−12 0.782
cg20295214 1 206,226,794 AVPR1B 1.47E−06 − 0.014 (0.003) 9.65E−07 − 0.011 (0.002) − 6.863 6.76E−12 0.766
cg23219570 12 4,488,893 FGF23 1.30E−05 0.012 (0.003) 8.52E−08 0.019 (0.004) 6.842 7.83E−12 ++ 0.346
cg26529655 5 424,371 AHRR 2.39E−06 − 0.011 (0.002) 7.37E−07 − 0.012 (0.002) − 6.827 8.68E−12 0.687
cg11554391 5 321,320 AHRR 6.57E−06 − 0.012 (0.003) 2.79E−07 − 0.015 (0.003) − 6.800 1.05E−11 0.495
cg25305703 8 128,378,218   1.26E−04 − 0.020 (0.005) 6.37E−09 − 0.037 (0.006) − 6.765 1.34E−11 0.103
cg09099830 16 30,485,485 ITGAL 1.42E−06 − 0.015 (0.003) 2.15E−06 − 0.017 (0.003) − 6.759 1.39E−11 0.860
cg10750182 10 73,497,514 CDH23 1.23E−07 − 0.012 (0.002) 2.98E−05 − 0.011 (0.003) − 6.715 1.88E−11 0.579
cg14580211 5 150,161,299 C5orf62 1.05E−05 − 0.020 (0.004) 3.19E−07 − 0.030 (0.006) − 6.709 1.96E−11 0.464
cg04180046 7 45,002,736 MYO1G 2.39E−05 0.027 (0.006) 1.35E−07 0.045 (0.008) 6.686 2.30E−11 ++ 0.330
cg17287155 5 393,347 AHRR 1.43E−05 − 0.010 (0.002) 3.74E−07 − 0.011 (0.002) − 6.639 3.15E−11 0.450
cg14316231 8 41,895,100 MYST3 2.32E−05 − 0.012 (0.003) 2.87E−07 − 0.026 (0.005) − 6.595 4.26E−11 0.386
cg03604011 5 400,201 AHRR 1.38E−07 0.012 (0.002) 7.92E−05 0.005 (0.001) 6.544 5.98E−11 ++ 0.479
cg09662411 1 92,946,132 GFI1 3.82E−05 − 0.025 (0.006) 3.56E−07 − 0.038 (0.007) − 6.484 8.93E−11 0.361
cg24996979 14 74,223,355 C14orf43 1.17E−04 − 0.009 (0.002) 1.20E−07 − 0.015 (0.003) − 6.428 1.29E−10 0.214
cg13751113 11 118,085,214 AMICA1 8.66E−06 − 0.011 (0.003) 5.27E−06 − 0.015 (0.003) − 6.359 2.03E−10 0.767
cg00310412 15 74,724,918 SEMA7A 3.66E−04 − 0.011 (0.003) 4.49E−08 − 0.020 (0.004) − 6.337 2.34E−10 0.117
cg18642234 3 49,394,622 GPX1 1.24E−06 − 0.013 (0.003) 4.44E−05 − 0.012 (0.003) − 6.331 2.43E−10 0.748
cg26361535 8 144,576,604 ZC3H3 9.58E−04 − 0.014 (0.004) 1.10E−08 − 0.029 (0.005) − 6.313 2.74E−10 0.054
cg00295485 2 106,755,721 UXS1 5.86E−05 − 0.017 (0.004) 7.63E−07 − 0.029 (0.006) − 6.311 2.77E−10 0.382
cg03440944 7 45,023,329 C7orf40 8.68E−08 − 0.012 (0.002) 4.66E−04 − 0.013 (0.004) − 6.301 2.96E−10 0.275
cg12075928 8 141,801,307 PTK2 4.90E−06 − 0.021 (0.005) 1.60E−05 − 0.026 (0.006) − 6.284 3.30E−10 0.969
cg01481251 11 32,912,719   5.67E−05 − 0.016 (0.004) 1.05E−06 − 0.012 (0.002) − 6.274 3.51E−10 0.410
cg03707168 19 49,379,127 PPP1R15A 1.16E−05 − 0.024 (0.006) 6.89E−06 − 0.027 (0.006) − 6.274 3.52E−10 0.766
cg11436113 20 19,191,145   1.29E−05 − 0.014 (0.003) 6.14E−06 − 0.018 (0.004) − 6.274 3.53E−10 0.741
cg00706683 2 233,251,030 ECEL1P2 7.54E−08 0.020 (0.004) 6.22E−04 0.016 (0.005) 6.267 3.69E−10 ++ 0.244
cg10062919 17 38,503,802 RARA 3.21E−05 − 0.008 (0.002) 2.37E−06 − 0.009 (0.002) − 6.259 3.86E−10 0.539
cg06394460 13 28,130,393 LNX2 8.32E−07 − 0.028 (0.006) 1.36E−04 − 0.019 (0.005) − 6.206 5.44E−10 0.568
cg04517079 6 41,546,161 FOXP4 1.28E−04 − 0.010 (0.002) 6.03E−07 − 0.014 (0.003) − 6.205 5.48E−10 0.300
cg16547579 20 4,954,333 SLC23A2 3.74E−04 − 0.011 (0.003) 1.39E−07 − 0.019 (0.004) − 6.194 5.87E−10 0.154
cg21446172 1 223,745,234 CAPN8 1.76E−04 − 0.010 (0.003) 4.68E−07 − 0.020 (0.004) − 6.180 6.40E−10 0.260
cg07251887 17 73,641,809 RECQL5 1.03E−07 − 0.016 (0.003) 8.91E−04 − 0.013 (0.004) − 6.158 7.38E−10 0.230
cg15474579 6 36,645,812 CDKN1A 1.01E−05 − 0.013 (0.003) 2.32E−05 − 0.018 (0.004) − 6.115 9.66E−10 0.934
cg16398761 14 74,220,238 C14orf43 1.58E−05 − 0.010 (0.002) 2.13E−05 − 0.013 (0.003) − 6.056 1.39E−09 0.870
cg13039251 5 32,018,601 PDZD2 4.03E−03 0.014 (0.005) 8.21E−09 0.040 (0.007) 6.035 1.59E−09 ++ 0.024
cg23110422 21 40,182,073 ETS2 5.94E−05 − 0.015 (0.004) 5.59E−06 − 0.020 (0.004) − 6.034 1.60E−09 0.560
cg02275418 3 15,372,726 SH3BP5 5.16E−05 − 0.009 (0.002) 7.61E−06 − 0.008 (0.002) − 6.013 1.82E−09 0.609
cg03188382 2 233,245,886 ALPP 3.42E−08 − 0.021 (0.004) 3.83E−03 − 0.012 (0.004) − 6.008 1.88E−09 0.099
cg14712058 19 16,988,083 SIN3B 1.93E−07 − 0.018 (0.003) 1.37E−03 − 0.012 (0.004) − 5.990 2.09E−09 0.226
cg03109660 4 37,684,505 RELL1 4.91E−06 − 0.013 (0.003) 1.05E−04 − 0.018 (0.005) − 5.987 2.14E−09 0.780
cg08035323 2 9,843,525   1.19E−03 0.017 (0.005) 1.31E−07 0.036 (0.007) 5.970 2.37E−09 ++ 0.099
cg13038618 14 77,467,391   1.08E−03 − 0.011 (0.003) 1.54E−07 − 0.020 (0.004) − 5.970 2.38E−09 0.108
cg03234777 11 118,095,544 AMICA1 4.97E−05 − 0.009 (0.002) 1.34E−05 − 0.011 (0.002) − 5.936 2.92E−09 0.677
cg13422817 12 4,550,927 FGF6 1.02E−05 0.011 (0.003) 7.28E−05 0.013 (0.003) 5.933 2.98E−09 ++ 0.913
cg15657641 11 47,939,769   1.73E−06 0.008 (0.002) 3.77E−04 0.007 (0.002) 5.923 3.17E−09 ++ 0.508
cg24851513 3 52,099,522 C3orf74 1.44E−04 0.007 (0.002) 4.37E−06 0.007 (0.002) 5.913 3.37E−09 ++ 0.444
cg17485141 2 42,566,556   8.57E−04 0.005 (0.002) 4.17E−07 0.014 (0.003) 5.890 3.86E−09 ++ 0.154
cg00385142 3 98,235,918 CLDND1 2.87E−07 − 0.009 (0.002) 1.81E−03 − 0.004 (0.001) − 5.881 4.09E−09 0.223
cg26764244 1 68,299,511 GNG12 1.68E−03 − 0.014 (0.004) 1.52E−07 − 0.026 (0.005) − 5.878 4.14E−09 0.090
cg01899089 5 369,969 AHRR 4.09E−08 − 0.016 (0.003) 6.94E−03 − 0.011 (0.004) − 5.854 4.80E−09 0.077
cg25013095 2 231,809,672   3.75E−08 − 0.008 (0.001) 7.93E−03 − 0.002 (0.001) − 5.835 5.39E−09 0.070
cg25292882 15 39,431,467   1.72E−04 − 0.011 (0.003) 6.24E−06 − 0.009 (0.002) − 5.829 5.57E−09 0.459
cg14179389 1 92,947,961 GFI1 6.93E−03 − 0.013 (0.005) 1.63E−08 − 0.033 (0.006) − 5.827 5.66E−09 0.022
cg09837977 7 110,731,201 LRRN3 8.75E−06 − 0.008 (0.002) 1.92E−04 − 0.006 (0.002) − 5.795 6.84E−09 0.760
cg16503724 3 17,130,667 PLCL2 2.95E−03 0.007 (0.002) 1.19E−07 0.020 (0.004) 5.786 7.22E−09 ++ 0.065
cg20454518 12 133,135,463 FBRSL1 2.88E−04 0.021 (0.006) 6.45E−06 0.028 (0.006) 5.728 1.01E−08 ++ 0.409
cg16382047 2 231,790,037 GPR55 6.89E−06 − 0.018 (0.004) 3.70E−04 − 0.023 (0.006) − 5.717 1.08E−08 0.643
cg06972908 16 30,488,321 ITGAL 1.26E−05 − 0.009 (0.002) 2.17E−04 − 0.013 (0.003) − 5.716 1.09E−08 0.784
cg00605777 2 97,533,635 SEMA4C 1.29E−05 − 0.009 (0.002) 2.47E−04 − 0.009 (0.003) − 5.690 1.27E−08 0.768
cg00300637 5 319,433 AHRR 9.94E−04 0.012 (0.004) 1.84E−06 0.021 (0.004) 5.661 1.50E−08 ++ 0.214
cg01882991 6 6,677,756   5.00E−05 − 0.010 (0.002) 8.16E−05 − 0.013 (0.003) − 5.653 1.58E−08 0.909
cg05049335 11 66,103,889 RIN1 4.95E−07 − 0.008 (0.002) 4.26E−03 − 0.007 (0.002) − 5.627 1.84E−08 0.180
cg10788371 11 76,381,040 LRRC32 6.06E−02 − 0.006 (0.003) 5.69E−10 − 0.024 (0.004) − 5.600 2.14E−08 0.001
cg04716530 16 30,485,684 ITGAL 3.32E−05 − 0.006 (0.002) 1.78E−04 − 0.009 (0.002) − 5.592 2.25E−08 0.928
cg09006487 3 72,424,982 RYBP 2.93E−09 − 0.023 (0.004) 6.83E−02 − 0.009 (0.005) − 5.584 2.35E−08 0.007
cg10841124 5 433,274 AHRR 2.42E−05 0.007 (0.002) 2.63E−04 0.013 (0.004) 5.577 2.45E−08 ++ 0.833
cg01956154 14 94,423,399 ASB2 3.59E−05 − 0.009 (0.002) 1.81E−04 − 0.009 (0.002) − 5.576 2.46E−08 0.936
cg26800893 11 67,184,596 ATPGD1 5.39E−05 0.008 (0.002) 1.21E−04 0.008 (0.002) 5.575 2.48E−08 ++ 0.955
cg05460226 17 8,804,279 PIK3R5 2.57E−−04 − 0.015 (0.004) 2.13E−05 − 0.029 (0.007) − 5.572 2.51E−08 0.538
cg18146737 1 92,946,700 GFI1 1.99E−04 − 0.036 (0.010) 3.50E−05 − 0.037 (0.009) − 5.543 2.97E−08 0.625
cg16201146 20 19,191,526   4.06E−07 − 0.012 (0.002) 7.10E−03 − 0.009 (0.003) − 5.541 3.01E−08 0.137
cg16814719 8 134,114,834 TG;SLA 4.48E−06 − 0.005 (0.001) 1.41E−03 − 0.005 (0.002) − 5.533 3.16E−08 0.427
cg00501876 3 39,193,251 CSRNP1 5.22E−04 − 0.009 (0.003) 1.15E−05 − 0.014 (0.003) − 5.529 3.22E−08 0.400
cg08763102 4 3,079,751 HTT 1.73E−03 − 0.007 (0.002) 2.13E−06 − 0.015 (0.003) − 5.525 3.30E−08 0.184
cg07381806 19 2,094,327 MOBKL2A 1.68E−03 − 0.015 (0.005) 2.62E−06 − 0.035 (0.007) − 5.502 3.75E−08 0.196
cg01731783 14 74,211,788 C14orf43 8.41E−07 − 0.008 (0.002) 5.40E−03 − 0.006 (0.002) − 5.500 3.81E−08 0.185
cg19717773 7 2,847,554 GNA12 1.86E−04 − 0.033 (0.009) 5.57E−05 − 0.043 (0.011) − 5.482 4.21E−08 0.691
cg17791651 1 38,513,489 POU3F1 4.05E−05 − 0.011 (0.003) 2.99E−04 − 0.012 (0.003) − 5.468 4.55E−08 0.876
cg23161492 15 90,357,202 ANPEP 6.62E−04 − 0.016 (0.005) 1.30E−05 − 0.026 (0.006) − 5.464 4.66E−08 0.387
cg07465627 17 53,167,407 STXBP4 3.03E−06 − 0.011 (0.002) 2.99E−03 − 0.013 (0.004) − 5.439 5.36E−08 0.311
cg16702313 14 74,251,926 C14orf43 4.78E−04 − 0.007 (0.002) 2.64E−05 − 0.008 (0.002) − 5.421 5.94E−08 0.490
cg07339236 20 50,312,490 ATP9A 5.74E−03 − 0.007 (0.003) 6.65E−07 − 0.014 (0.003) − 5.411 6.27E−08 0.080
cg15187398 19 2,093,896 MOBKL2A 2.94E−03 − 0.011 (0.004) 2.10E−06 − 0.019 (0.004) − 5.410 6.29E−08 0.150
cg02743070 10 80,834,309 ZMIZ1 7.44E−05 − 0.007 (0.002) 2.35E−04 − 0.009 (0.002) − 5.406 6.45E−08 0.990
cg20059928 15 40,361,485   4.01E−05 − 0.025 (0.006) 5.01E−04 − 0.021 (0.006) − 5.377 7.57E−08 0.798
cg14120703 9 139,416,102 NOTCH1 4.33E−05 − 0.008 (0.002) 4.80E−04 − 0.008 (0.002) − 5.372 7.79E−08 0.814
cg11816838 3 150,484,093   1.33E−02 − 0.006 (0.002) 1.81E−07 − 0.009 (0.002) − 5.369 7.90E−08 0.033
cg26057754 1 183,774,231 RGL1 6.85E−06 − 0.004 (0.001) 2.32E−03 − 0.003 (0.001) − 5.367 8.01E−08 0.400
cg19713851 2 233,246,594 ALPP 5.33E−05 − 0.031 (0.008) 4.12E−04 − 0.032 (0.009) − 5.364 8.13E−08 0.863
cg03519879 14 74,227,499 C14orf43 8.89E−07 − 0.008 (0.002) 9.74E−03 − 0.006 (0.002) − 5.357 8.46E−08 0.144