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Table 4 Discordant CpG sites between MC-seq and EPIC (difference>0.5)

From: Comparison of methylation capture sequencing and Infinium MethylationEPIC array in peripheral blood mononuclear cells

Probe Chr Position Gene MC-seq median EPIC median Median Difference between MC-seq and EPIC Refgene group Relation to CpG island
cg09156519 9 103361572   0.009 0.960 0.95   S_Shore
cg18176117 9 96097296 C9orf129 0.000 0.932 0.93 Body N_Shore
cg14268958 10 133453066   0.000 0.899 0.89   S_Shelf
cg10576280 10 124133822 PLEKHA1 0.072 0.948 0.88 TSS1500 N_Shore
cg01005486 3 13246006   0.047 0.886 0.84   Island
cg23433318 19 667542   0.007 0.866 0.84   Island
cg10766172 7 27498479   0.989 0.147 0.82   
cg11812439 4 68928706 LOC550113;SYT14P1;TMPRSS11F 0.973 0.155 0.82 Body; Body; Body  
cg23950473 5 154393265 KIF4B; KIF4B 0.992 0.174 0.82 1stExon; 5’UTR  
cg00259849 8 4183880 CSMD1 0.000 0.821 0.82 Body  
cg23981150 1 161111090   1.000 0.217 0.78   Island
cg09698465 12 133000178   0.906 0.080 0.78   Island
cg20450977 11 10529463 MTRNR2L8; MTRNR2L8 0.964 0.189 0.77 3’UTR; 1stExon  
cg01053463 1 26186087 C1orf135 0.021 0.757 0.76 TSS1500 Island
cg12499827 2 202004893 CFLAR; CFLAR; CFLAR; CFLAR; CFLAR; CFLAR; CFLAR; CFLAR; CFLAR 0.971 0.215 0.76 TSS200; Body; Body; Body; Body; Body; Body; Body; Body  
cg03133777 2 170361364 BBS5 1.000 0.244 0.75 3’UTR  
cg19040702 17 22023833   0.969 0.230 0.75   
cg21675871 11 69813397   0.217 0.960 0.74   Island
cg04240493 3 148414664 AGTR1; AGTR1; AGTR1; AGTR1 0.979 0.258 0.72 TSS1500; TSS1500; TSS1500; TSS1500 N_Shore
cg16889427 10 127584375 FANK1 0.036 0.759 0.71 TSS1500 Island
cg25916505 18 32820654 ZNF397; ZNF397 0.000 0.711 0.71 TSS1500; TSS1500 N_Shore
cg13525026 17 18061071 MYO15A 1.000 0.290 0.71 Body  
cg07825433 4 1215099 CTBP1; CTBP1 0.000 0.716 0.71 Body; Body N_Shelf
cg03846641 2 109746751 LOC100287216; SH3RF3 0.239 0.952 0.71 TSS200; Body Island
cg19188207 2 10340837 C2orf48 1.000 0.290 0.71 Body  
cg11495544 17 73402155 GRB2; GRB2 0.753 0.049 0.70 TSS1500; TSS1500 S_Shore
cg06931905 8 42036940 PLAT; PLAT 0.896 0.197 0.70 Body; Body  
cg03348902 1 569603   0.869 0.168 0.70   
cg27120934 6 129480619 LAMA2; LAMA2 0.979 0.297 0.69 Body; Body  
cg07576219 1 55012408 ACOT11; ACOT11 0.927 0.250 0.69 TSS1500; TSS1500 S_Shelf
cg08400246 5 156570642 MED7; MED7 0.153 0.870 0.68 TSS1500; TSS1500 S_Shore
cg27626141 8 103876469 AZIN1; AZIN1 0.000 0.682 0.68 TSS200; TSS200 Island
cg26688472 2 203638928 ICA1L 0.984 0.303 0.68 3’UTR Island
cg26101183 10 65930786   0.957 0.279 0.68   Island
cg27090007 13 28519388 ATP5EP2 0.985 0.321 0.67 Body  
cg11896012 19 53696753 ZNF665 0.048 0.700 0.67 TSS200 S_Shore
cg02606018 12 10658281   0.979 0.323 0.66   
cg00438164 4 100870480 H2AFZ; LOC256880 0.004 0.650 0.65 Body; TSS1500 Island
cg21164300 9 136098495   0.000 0.644 0.64   N_Shelf
cg15891076 10 65930618   0.971 0.328 0.64   Island
cg05948389 5 1641924   0.014 0.660 0.64   N_Shelf
cg10507965 10 102107251 SCD; SCD 0.011 0.642 0.64 5’UTR; 1stExon Island
cg21662326 11 14521493 COPB1; COPB1; COPB1 0.643 0.012 0.63 TSS200; TSS200; TSS200  
cg09646578 8 5019363   0.310 0.934 0.63   
cg24717964 20 61477008 DPH3B; DPH3B; TCFL5 0.986 0.356 0.63 1stExon; 5’UTR; Body  
cg07437919 8 142234483 SLC45A4 0.957 0.313 0.63 Body N_Shore
cg01105403 2 240723304   0.050 0.890 0.63   
cg20482143 7 64340804   0.982 0.346 0.63   
cg11187452 22 49698612   0.017 0.653 0.63   Island
cg24504954 3 61237217 FHIT; FHIT 0.017 0.649 0.62 TSS200; TSS200 Island
cg27434351 11 14521491 COPB1; COPB1; COPB1 0.639 0.016 0.62 TSS200; TSS200; TSS200  
cg15864074 2 120974042   0.976 0.354 0.62   
cg00913521 12 89893799 WDR51B 0.977 0.339 0.62 Body  
cg27534567 1 568536   0.834 0.262 0.62   
cg24515136 17 49024834   0.949 0.328 0.62   S_Shelf
cg01417615 1 52456419 RAB3B 0.629 0.015 0.61 TSS200 Island
cg00236302 12 69004867 RAP1B; RAP1B 0.000 0.612 0.61 5’UTR; 5’UTR Island
cg10747603 22 29197018 XBP1; XBP1 0.022 0.627 0.61 TSS1500; TSS1500 S_Shore
cg03594447 1 20359744   1.000 0.358 0.61   
cg23045277 4 190587808   0.299 0.910 0.61   
cg02218809 16 29973300 TMEM219; TMEM219 0.020 0.612 0.61 TSS200; TSS200 Island
cg05646491 10 135379754 SYCE1; SYCE1; SYCE1 0.988 0.382 0.60 TSS1500; 5’UTR; TSS1500 Island
cg07596174 20 55926107 RAE1; RAE1 0.014 0.613 0.60 TSS1500; TSS200 N_Shore
cg03543448 16 4384967 GLIS2 0.927 0.315 0.60 Body  
cg25793197 5 31923469 PDZD2 0.976 0.379 0.60 Body  
cg21392229 2 161223778 RBMS1; RBMS1 1.000 0.384 0.60 Body; Body  
cg05607320 12 53342553 KRT18; KRT18 0.064 0.651 0.60 TSS200; TSS1500 N_Shore
cg13896861 9 94878241 SPTLC1; SPTLC1 0.117 0.711 0.60 TSS1500; TSS1500 S_Shore
cg03064900 4 190566141   0.323 0.921 0.60   N_Shore
cg16199859 3 75263685   0.861 0.276 0.60   
cg15006843 1 205720633 NUCKS1 0.880 0.260 0.60 TSS1500 S_Shore
cg02498218 4 26361371 RBPJ; RBPJ; RBPJ; RBPJ 0.979 0.388 0.59 Body; Body; 5’UTR; Body Island
cg07116712 15 96887959   0.091 0.681 0.59   Island
cg11643306 20 34204831 SPAG4 0.038 0.630 0.59 Body S_Shore
cg08568561 7 42834498   0.981 0.392 0.59   
cg06669598 6 127622363 ECHDC1; ECHDC1; ECHDC1; ECHDC1; ECHDC1 0.984 0.351 0.59 3’UTR; 3’UTR; Body; Body; Body  
cg22805431 3 113955600 ZNF80 0.983 0.409 0.59 1stExon  
cg24636332 17 4437925 SPNS2 0.301 0.939 0.59 Body N_Shore
cg05924191 15 35279830 ZNF770 0.008 0.605 0.59 5’UTR N_Shore
cg14402194 14 23398944 PRMT5; PRMT5; PRMT5; PRMT5; PRMT5; PRMT5; LOC101926933 0.028 0.592 0.58 TSS200; TSS200; TSS200; TSS200; TSS200; TSS200; Body S_Shore
cg01737532 4 190862170 FRG1 0.000 0.584 0.58 1stExon Island
cg25744017 15 52819324 MYO5A; MYO5A 0.957 0.379 0.58 Body;Body N_Shore
cg03432151 15 89745000 ABHD2; ABHD2 0.948 0.360 0.58 3’UTR; 3’UTR  
cg27196695 10 134571377 INPP5A 1.000 0.420 0.58 Body  
cg27571351 10 17619364   0.986 0.407 0.58   
cg02775804 2 120974080   0.977 0.401 0.58   
cg16461530 10 134798264   0.664 0.106 0.58   
cg12654770 10 52487693   0.962 0.385 0.58   
cg16112880 1 201123745 TMEM9 0.003 0.579 0.58 TSS200 Island
cg20641423 8 125315065   0.911 0.338 0.57   S_Shore
cg23248615 10 2005709   0.905 0.313 0.57   
cg25550279 7 53254983   0.965 0.381 0.57   Island
cg01070250 1 569687   0.843 0.271 0.57   
cg06977575 4 139481990   0.953 0.376 0.57   Island
cg14511644 9 15055021   0.977 0.399 0.57   
cg08947542 8 35383200 UNC5D 0.879 0.309 0.57 Body  
cg10258063 2 217363243 RPL37A 0.043 0.613 0.57 TSS1500 N_Shore
cg24209723 18 12913133   0.973 0.399 0.57   S_Shore
cg02265379 5 87898506 LOC645323 0.971 0.384 0.57 Body Island
cg18925601 7 158752715   0.006 0.574 0.57   Island
cg01406075 11 58731104   0.885 0.309 0.57   N_Shore
cg13545297 12 54404315 HOXC8 0.229 0.791 0.57 Body S_Shore
cg09036531 10 96991505   0.968 0.402 0.57   
cg25649283 9 140714075 EHMT1 0.382 0.950 0.57 Body Island
cg06204030 17 7792051 CHD3; CHD3; CHD3 0.761 0.141 0.57 TSS200; TSS200; Body S_Shelf
cg18627328 19 621561 POLRMT 0.980 0.411 0.56 Body Island
cg13085681 8 48920761 UBE2V2 0.009 0.576 0.56 TSS1500 N_Shore
cg00999469 6 25107287 CMAHP 0.043 0.931 0.56 Body  
cg20960039 9 130213605 LRSAM1; RPL12; LRSAM1; LRSAM1; LRSAM1; RPL12 0.020 0.582 0.56 TSS1500; 1stExon; TSS200; TSS200; TSS200; 5’UTR Island
cg04400841 2 208988863 CRYGD 0.215 0.764 0.56 Body Island
cg12476298 19 58426697 ZNF417 0.977 0.407 0.56 Body N_Shore
cg23997402 19 14275669 LPHN1; LPHN1 0.972 0.442 0.56 Body; Body S_Shore
cg16935370 5 154393281 KIF4B; KIF4B 0.981 0.414 0.56 1stExon; 5′UTR  
cg04222159 1 204981786 NFASC; NFASC; NFASC; NFASC 0.630 0.073 0.56 Body; Body; Body; Body  
cg06396237 8 120779442 TAF2 0.985 0.430 0.56 Body  
cg06599543 6 165749446 PDE10A;PDE10A 0.857 0.332 0.56 Body;Body S_Shore
cg11566832 10 88659593 BMPR1A 0.145 0.693 0.55 Body  
cg20334010 15 41047916 RMDN3; RMDN3 0.020 0.570 0.55 TSS1500; TSS1500 S_Shore
cg18245781 5 3659697   0.283 0.852 0.55   
cg03761810 2 10264850 RRM2; RRM2 0.018 0.567 0.55 Body; Body S_Shore
cg02122372 3 149657597 RNF13; RNF13 1.000 0.439 0.55 Body; Body  
cg06753227 18 9475508 RALBP1 0.000 0.553 0.55 TSS200 Island
cg14131834 13 45914250 LOC100190939; TPT1 0.040 0.594 0.55 TSS1500; Body N_Shore
cg25583180 5 177614382 GMCL1L 1.000 0.451 0.55 Body Island
cg09112623 6 33756905 LEMD2; LEMD2 0.568 0.019 0.55 5’UTR; 1stExon Island
cg11759477 4 190861959 FRG1 0.000 0.548 0.55 TSS200 Island
cg12796755 14 51132292 SAV1 0.932 0.383 0.55 Body N_Shelf
cg19693446 14 102144192   0.958 0.407 0.55   
cg25187648 3 49395165 GPX1; GPX1; GPX1 0.018 0.568 0.55 Body; 3’UTR; 1stExon Island
cg20391833 6 167116208 RPS6KA2 0.964 0.431 0.55 Body  
cg09705232 6 97611802 MIR548H3; C6orf167 0.974 0.428 0.55 Body; Body  
cg04643437 12 14518655 ATF7IP; ATF7IP 0.000 0.561 0.55 1stExon; 5’UTR Island
cg17558062 13 45965415 LOC100190939 1.000 0.456 0.54 Body Island
cg26825848 4 190566175   0.350 0.899 0.54   N_Shore
cg13943141 9 93205862   0.846 0.296 0.54   
cg26951705 19 56612697 ZNF787 0.000 0.542 0.54 Body Island
cg24654094 1 160340832 NHLH1 0.964 0.433 0.54 Body Island
cg02996355 14 81879375   0.909 0.364 0.54   
cg11914812 12 56904792   1.000 0.459 0.54   
cg24895977 19 35861796   0.990 0.450 0.54   
cg11637682 6 147124984 LOC729176; C6orf103 0.867 0.300 0.54 TSS200; Body  
cg07089633 14 73396378 DCAF4; DCAF4; DCAF4; DCAF4; DCAF4 1.000 0.450 0.54 5’UTR; 5’UTR; 5’UTR; 5’UTR; 5’UTR S_Shelf
cg20360416 4 7246127 SORCS2 0.018 0.659 0.54 Body  
cg25627920 17 39992620 NT5C3B; NT5C3B; NT5C3B; KLHL10 0.016 0.552 0.54 TSS200; TSS200; TSS200; TSS1500 Island
cg24000259 5 55488291 ANKRD55 0.961 0.411 0.54 Body  
cg09138437 11 64527189 PYGM; PYGM 0.993 0.445 0.54 1stExon; 1stExon  
cg02673636 1 109647056   0.976 0.437 0.54   S_Shelf
cg18740872 5 39220260 FYB; FYB 1.000 0.466 0.53 TSS1500; TSS1500  
cg14354292 7 63353606   0.960 0.426 0.53   
cg17704839 19 9939038 UBL5; UBL5 0.014 0.542 0.53 Body; Body S_Shore
cg05971373 7 157498604 PTPRN2; PTPRN2; PTPRN2 1.000 0.467 0.53 Body; Body; Body S_Shelf
cg05291429 17 1494566 SLC43A2 0.402 0.969 0.53 Body S_Shelf
cg08841342 3 156528470 PA2G4P4 0.976 0.444 0.53 Body  
cg04096697 6 37012867   0.983 0.451 0.53   Island
cg26878995 1 168106731 GPR161 0.052 0.570 0.53 TSS1500 S_Shore
cg24031524 20 19804606   0.990 0.468 0.53   
cg19311470 4 39460490 RPL9; RPL9; LIAS; LIAS 0.004 0.529 0.53 TSS1500; 5’UTR; TSS200; TSS200 Island
cg02181482 5 178942685   0.956 0.449 0.53   
cg05346902 19 47910374 MEIS3; MEIS3 0.068 0.593 0.53 Body; Body Island
cg16470772 10 8203304   0.971 0.445 0.53   
cg10115022 1 27527942   0.974 0.464 0.53   Island
cg27231717 6 26319377   0.905 0.386 0.53   
cg09451549 19 8386408 RPS28; NDUFA7; RPS28 0.000 0.527 0.53 5’UTR; TSS200; 1stExon Island
cg07628841 2 27851430 GPN1; CCDC121; GPN1; GPN1; CCDC121; CCDC121; GPN1; GPN1 0.010 0.536 0.53 TSS200; 1stExon; TSS200; TSS1500; 5’UTR; 1stExon; TSS200; TSS1500  
cg03816081 10 29577743 LYZL1 0.863 0.301 0.52 TSS1500  
cg00762003 21 45393541 AGPAT3; AGPAT3 0.383 0.892 0.52 Body; Body Island
cg19466922 7 130138026 MEST; MEST; MEST; MEST; MEST; MEST 1.000 0.476 0.52 Body; Body; Body; Body; Body; Body  
cg07712165 17 80899280 TBCD 0.440 0.959 0.52 Body Island
cg01199952 13 25591486   0.984 0.456 0.52   N_Shore
cg11374834 3 75263691   0.950 0.428 0.52   
cg02974491 1 1162280 SDF4; SDF4 0.403 0.964 0.52 Body; Body Island
cg10555853 1 33516627   0.929 0.407 0.52   Island
cg21216606 2 207275704   0.985 0.464 0.52   
cg17711541 6 26124704 HIST1H2AC; HIST1H2BC 0.007 0.529 0.52 1stExon; TSS1500 Island
cg06412823 7 22541074 STEAP1B; STEAP1B 0.196 0.739 0.52 TSS1500; TSS1500 S_Shore
cg03054343 11 50238214   1.000 0.463 0.52   Island
cg05766605 1 19384827   0.423 0.938 0.52   
cg07684215 10 132976057 TCERG1L 0.181 0.923 0.52 Body  
cg27193858 6 41169120 TREML2 0.181 0.691 0.52 TSS200  
cg00964321 16 15083956 PDXDC1 0.906 0.386 0.52 Body Island
cg25394572 11 56457777 OR8U8 0.949 0.429 0.52 Body  
cg10667969 3 149181941   0.967 0.458 0.52   
cg18394854 5 8457818   0.212 0.732 0.52   Island
cg05741225 10 133917303 JAKMIP3 0.906 0.370 0.52 TSS1500  
cg06026769 12 20704492 PDE3A 0.993 0.473 0.52 Body N_Shore
cg09032630 6 27831956 HIST1H2AL 0.802 0.311 0.52 TSS1500 N_Shore
cg16626480 22 25575426 KIAA1671 0.950 0.422 0.52 Body Island
cg24534731 17 36888147 CISD3 0.969 0.457 0.52 Body S_Shore
cg16202259 14 104625420 KIF26A 0.058 0.962 0.52 Body Island
cg25325592 8 1439535   0.408 0.923 0.52   N_Shore
cg00391025 3 100427239 TFG; TFG 1.000 0.477 0.52 TSS1500; TSS1500 N_Shore
cg25149037 17 39736213   0.820 0.454 0.52   
cg19120749 11 1431650 BRSK2; BRSK2; BRSK2; BRSK2; BRSK2; BRSK2 0.468 0.983 0.52 TSS1500; TSS200; Body; Body; Body; Body Island
cg24270624 10 95721318 PIPSL 0.947 0.421 0.52 Body  
cg16346588 10 242978 ZMYND11; ZMYND11; ZMYND11 0.970 0.459 0.51 Body; Body; Body  
cg02750322 15 83673816 C15orf40; C15orf40; C15orf40; C15orf40; C15orf40 0.966 0.451 0.51 Body; 3’UTR; Body; Body; Body  
cg04363536 3 49466872 NICN1 0.000 0.515 0.51 TSS200 S_Shore
cg17883371 1 91359225   1.000 0.480 0.51   Island
cg25018832 1 564471 LOC101928626 0.602 0.088 0.51 TSS200  
cg16838729 4 43901032   0.903 0.394 0.51   
cg23222247 17 47302219 PHOSPHO1; PHOSPHO1 0.009 0.531 0.51 Body;Body Island
cg19496566 19 48249018 GLTSCR2 0.009 0.535 0.51 1stExon Island
cg03165426 7 30726958 CRHR2; CRHR2 0.429 0.942 0.51 Body; 5’UTR  
cg19600494 2 106959525   0.968 0.455 0.51   Island
cg10854807 17 79479308 ACTG1 0.004 0.522 0.51 Body Island
cg20699097 11 111957680 TIMM8B; TIMM8B; SDHD 0.009 0.524 0.51 TSS200; TSS200; 1stExon Island
cg22819767 10 11866910 C10orf47 0.958 0.440 0.51 5’UTR S_Shore
cg20254251 8 144557206 ZC3H3 0.993 0.450 0.51 Body  
cg00590830 1 32385224 PTP4A2; PTP4A2; PTP4A2; PTP4A2; PTP4A2 0.971 0.437 0.51 1stExon; 1stExon; 5’UTR; 5’UTR; 5’UTR  
cg03877767 2 11680057 GREB1; GREB1 0.172 0.683 0.51 5’UTR; TSS200  
cg00487526 15 90818384   0.956 0.444 0.51   Island
cg17501384 2 217364031 RPL37A 0.017 0.521 0.51 Body S_Shore
cg17646418 6 166911767 RPS6KA2; RPS6KA2 0.987 0.468 0.51 Body; Body  
cg06757405 5 140789450 PCDHGA4; PCDHGA9; PCDHGA1; PCDHGB1; PCDHGB6; PCDHGB6; PCDHGB3; PCDHGA6; PCDHGA8; PCDHGA5; PCDHGB4; PCDHGA3; PCDHGA2; PCDHGB2; PCDHGA7; PCDHGB5 0.108 0.607 0.51 Body; Body; Body; Body; 1stExon; 1stExon; Body; Body; Body; Body; Body; Body; Body; Body; Body; Body Island
cg13448596 8 2031599 MYOM2 0.381 0.887 0.51 Body  
cg16711165 11 111957658 TIMM8B; TIMM8B; SDHD 0.017 0.522 0.51 TSS200; TSS200; 1stExon Island
cg16786640 4 3485263 DOK7; DOK7 0.447 0.954 0.51 Body; Body N_Shore
cg07638938 10 131348599 MGMT 0.986 0.492 0.51 Body  
cg05407710 8 143329409 TSNARE1 0.960 0.451 0.51 Body N_Shelf
cg07869994 3 174095190   0.988 0.482 0.51   Island
cg07455406 14 21077527   0.017 0.523 0.51   N_Shore
cg04576847 17 12623611 MYOCD; MYOCD; MYOCD; MYOCD 0.958 0.447 0.51 Body; 5’UTR; Body; 1stExon  
cg15699853 18 57684747   0.976 0.467 0.51   
cg11231240 8 82434638   1.000 0.482 0.51   Island
cg06157924 4 942005 TMEM175 0.451 0.957 0.51 Body S_Shore
cg23679141 4 165118930 MARCH1; ANP32C 0.946 0.445 0.51 5’UTR; TSS200  
cg03053358 17 1029917 ABR; ABR 0.446 0.964 0.51 Body; 5’UTR S_Shore
cg13705894 9 138305338   0.978 0.495 0.51   S_Shore
cg18512780 17 76117734 TMC6; TMC6 0.033 0.529 0.50 Body; Body  
cg06307940 16 46660818   0.986 0.487 0.50   
cg15541008 5 95297508 ELL2; ELL2 0.000 0.516 0.50 1stExon; 5’UTR S_Shore
cg19969624 13 95954210 ABCC4; ABCC4; ABCC4; ABCC4 0.011 0.507 0.50 TSS1500; TSS1500; TSS1500; TSS1500 Island
cg01758870 7 23719630 C7orf46; C7orf46; C7orf46 0.028 0.545 0.50 TSS200;TSS200;TSS200 Island
cg08323201 15 101835348 SNRPA1 0.000 0.503 0.50 1stExon Island
cg21863998 11 19770288 NAV2; NAV2; NAV2 0.439 0.905 0.50 Body; Body; Body  
cg11471802 8 47529015   0.348 0.882 0.50   Island
cg22281935 2 162934111   0.982 0.481 0.50   S_Shelf
cg06032540 15 43941563 CATSPER2; CATSPER2; CATSPER2 1.000 0.500 0.50 TSS1500; TSS1500; TSS1500 Island
cg18761878 1 568475   0.893 0.401 0.50   
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