Table 2.
Overlapping Genomic Coordinates with Differential Methylation in Nine Conditions Compared to Control Subjects
| Chr | Disease 1 | Coordinates 1 | Methylation Difference 1 | Probes 1 | Disease 2 | Coordinates 2 | Methylation Difference 2 | Probes 2 | Direction of Change | Overlapping Gene(s) | Distance to CpG Island (bp) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 19 | Floating-Harbor | 8591364–8591776 | −0.4 | 4 | Kabuki | 8591364–8591776 | −0.28 | 4 | same | MYO1F | 0 |
| 11 | Floating-Harbor | 65360123–65360327 | −0.27 | 3 | Kabuki | 65360123–65360327 | −0.19 | 3 | same | KCNK7 | 0 |
| 1 | Sotos | 227746111–227747468 | −0.35 | 7 | Kabuki | 227746191–227746882 | 0.14 | 4 | opposite | – | 0 |
| 3 | Sotos | 49170496–49171051 | −0.22 | 7 | Kabuki | 49170599–49170794 | 0.16 | 4 | opposite | LAMB2 | 12,032 |
| 5 | Sotos | 1856325–1857828 | −0.2 | 7 | Kabuki | 1856713–1857477 | 0.16 | 4 | opposite | – | 0 |
| 12 | Sotos | 133179887–133180698 | −0.25 | 5 | Kabuki | 133179887–133180238 | 0.11 | 4 | opposite | LRCOL1 | 0 |
| 5 | Sotos | 101119084–101119766 | −0.24 | 5 | Kabuki | 101119084–101119566 | 0.11 | 4 | opposite | – | 512,283 |
| 7 | Sotos | 27170241–27170552 | 0.19 | 6 | Kabuki | 27170388–27170994 | −0.14 | 13 | opposite | HOXA4 | 0 |
| 19 | Sotos | 51330265–51330469 | −0.24 | 4 | Kabuki | 51330265–51330469 | 0.13 | 4 | opposite | KLK15 | 0 |
| 15 | Sotos | 29968032–29968195 | −0.3 | 3 | Kabuki | 29968032–29968195 | 0.18 | 3 | opposite | – | 410 |
| 7 | Sotos | 27170717–27171051 | 0.15 | 9 | Kabuki | 27170388–27170994 | −0.14 | 13 | opposite | – | 78 |
| 2 | Sotos | 109746691–109747003 | −0.21 | 5 | Kabuki | 109746691–109746754 | −0.14 | 4 | same | SH3RF3 | 0 |
| 7 | Sotos | 142494148 - 142494492 | −0.16 | 6 | Kabuki | 142494148–142494492 | −0.15 | 6 | same | – | 71 |
| 5 | Sotos | 176827082–176827697 | −0.16 | 5 | Kabuki | 176827392–176827697 | −0.16 | 3 | same | PFN3 | 0 |
| 10 | Sotos | 132099067–132100019 | −0.17 | 3 | Kabuki | 132099067–132100019 | 0.15 | 3 | opposite | – | 109,734 |
| 7 | CHARGE | 27182493–27183946 | 0.23 | 20 | Kabuki | 27182493–27183816 | 0.16 | 18 | same | HOXA5, HOXA-AS3 | 0 |
| 7 | CHARGE | 27184316–27184521 | 0.17 | 8 | Kabuki | 27184369–27184441 | 0.14 | 4 | same | HOXA-AS3 | 0 |
| 17 | Floating-Harbor | 7486551–7486874 | −0.24 | 7 | Claes–Jensen | 7486551–7486874 | −0.29 | 7 | same | – | 0 |
| 1 | Sotos | 247694041–247694531 | −0.25 | 6 | Claes–Jensen | 247694041–247694531 | −0.24 | 6 | same | GCSAML,GCSAML-AS1, OR2C3 | 0 |
| 5 | Sotos | 176559334–176559563 | −0.36 | 3 | Claes–Jensen | 176559334–176559563 | −0.32 | 3 | same | – | 0 |
| 13 | Sotos | 113242878–113243141 | −0.21 | 3 | Claes–Jensen | 113242878–113243141 | −0.32 | 3 | same | TUBGCP3 (396bp away) | 221 |
| 6 | Sotos | 32120625–32121433 | −0.31 | 27 | Floating-Harbor | 32120773–32120933 | −0.15 | 10 | same | – | 396 |
| 6 | Sotos | 31650735–31651249 | −0.17 | 17 | Floating-Harbor | 31650735–31650835 | −0.19 | 6 | same | – | 0 |
| 6 | Sotos | 31650735–31651249 | −0.17 | 17 | Floating-Harbor | 31650916–31651278 | −0.15 | 11 | same | – | 0 |
| 6 | Sotos | 32847702–32847845 | −0.29 | 10 | Floating-Harbor | 32847702–32847845 | 0.18 | 10 | opposite | – | 0 |
| 17 | Sotos | 36997420–36997740 | −0.38 | 7 | Floating-Harbor | 36997420–36997740 | −0.23 | 7 | same | C17orf98 | 0 |
| 8 | Sotos | 39171866–39172120 | −0.31 | 7 | Floating-Harbor | 39172020–39172120 | 0.2 | 6 | opposite | ADAM5 (61bp away) | 206,442 |
| 10 | Sotos | 50649666–50650248 | −0.39 | 5 | Floating-Harbor | 50649666–50650248 | 0.18 | 5 | opposite | – | 42,882 |
| 6 | Sotos | 33282867–33283055 | −0.16 | 12 | Floating-Harbor | 33282867–33283184 | −0.18 | 19 | same | – | 0 |
| 2 | Sotos | 129659018–129659946 | −0.24 | 7 | Floating-Harbor | 129659316–129659946 | 0.19 | 6 | opposite | – | 0 |
| 5 | Sotos | 83016779–83017553 | −0.25 | 6 | Floating-Harbor | 83017000–83017644 | 0.19 | 6 | opposite | HAPLN1 | 341 |
| 4 | Sotos | 11369349–11370872 | −0.18 | 8 | Floating-Harbor | 11370314–11370565 | 0.25 | 3 | opposite | MIR572 | 0 |
| 8 | Sotos | 102235927–102236831 | −0.23 | 6 | Floating-Harbor | 102236283–102236831 | 0.23 | 5 | opposite | – | 0 |
| 2 | Sotos | 165811816–165812159 | −0.26 | 5 | Floating-Harbor | 165811816–165812159 | 0.22 | 5 | opposite | SLC38A11 | 112,922 |
| 7 | Sotos | 92672812–92673176 | −0.25 | 5 | Floating-Harbor | 92672812–92673176 | 0.2 | 5 | opposite | – | 0 |
| 4 | Sotos | 155702409–155703138 | −0.18 | 6 | Floating-Harbor | 155702409–155703138 | 0.19 | 6 | opposite | RBM46 | 0 |
| 1 | Sotos | 1003126–1003529 | −0.25 | 4 | Floating-Harbor | 1003126–1003529 | −0.29 | 4 | same | – | 0 |
| 3 | Sotos | 159557552–159558031 | −0.24 | 4 | Floating-Harbor | 159557552–159558031 | 0.23 | 4 | opposite | SCHIP1, IQCJ-SCHIP1 | 74,528 |
| 2 | Sotos | 164204628–164204915 | −0.24 | 4 | Floating-Harbor | 164204752–164205343 | 0.31 | 6 | opposite | – | 0 |
| 22 | Sotos | 50737978–50738890 | −0.22 | 4 | Floating-Harbor | 50737978–50738890 | −0.29 | 4 | same | PLXNB2 | 0 |
| 12 | Sotos | 56617576–56617737 | −0.28 | 3 | Floating-Harbor | 56617576–56617737 | −0.23 | 3 | same | – | 258 |
| 9 | Sotos | 139258524–139259074 | −0.26 | 3 | Floating-Harbor | 139258524–139259074 | −0.23 | 3 | same | CARD9 | 0 |
| 19 | Sotos | 3480363–3480672 | −0.21 | 5 | Floating-Harbor | 3480363–3480672 | −0.2 | 5 | same | SMIM24 | 1,110 |
| 19 | Sotos | 49222892–49223278 | −0.2 | 5 | Floating-Harbor | 49222892–49223278 | −0.28 | 5 | same | MAMSTR | 0 |
| 4 | Sotos | 165898666–165898848 | −0.19 | 5 | Floating-Harbor | 165898666–165898848 | 0.19 | 5 | opposite | TRIM61 | 20,219 |
| 1 | Sotos | 45278971–45279349 | −0.21 | 4 | Floating-Harbor | 45278971–45279349 | −0.23 | 4 | same | BTBD19 | 0 |
| 19 | Sotos | 2428350–2428677 | −0.19 | 4 | Floating-Harbor | 2428350–2429209 | −0.2 | 6 | same | LMNB2 | 0 |
| 19 | Sotos | 1063624–1064218 | −0.19 | 3 | Floating-Harbor | 1063624–1064218 | −0.24 | 3 | same | ABCA7 | 0 |
| 4 | Sotos | 46126066–46126253 | −0.18 | 3 | Floating-Harbor | 46126066–46126448 | 0.25 | 7 | opposite | GABRG1 | 265,650 |
| 12 | Sotos | 47219737–47219958 | −0.14 | 9 | Floating-Harbor | 47219626–47219920 | 0.18 | 9 | opposite | SLC38A4 | 4,954 |
| 5 | Sotos | 110062384–110062837 | −0.16 | 6 | Floating-Harbor | 110062384–110062837 | 0.23 | 6 | opposite | TMEM232 | 11,768 |
| 11 | Sotos | 32449254–32449638 | −0.17 | 3 | ADCA-DN | 32449163–32450692 | 0.24 | 11 | opposite | WT1 | 0 |
| 7 | CHARGE | 27137922–27138712 | −0.15 | 4 | Sotos | 27137922–27138396 | −0.17 | 3 | same | HOTAIRM1 | 1,185 |
| 7 | CHARGE | 53254947–53255065 | 0.15 | 3 | Sotos | 53254947–53255065 | 0.18 | 3 | same | – | 0 |
| 5 | CHARGE | 161178574–161178796 | 0.14 | 3 | Sotos | 161178574–161178796 | 0.17 | 3 | same | – | 203,189 |
| 5 | ATRX | 23507450–23507752 | −0.26 | 10 | Sotos | 23507573–23507656 | −0.22 | 5 | same | PRDM9 | 1,682,751 |
| 15 | ATRX | 39871808–39872186 | −0.26 | 6 | Sotos | 39871876–39872186 | −0.16 | 5 | same | – | 341 |
| 3 | ATRX | 109056349–109056897 | 0.29 | 4 | Sotos | 109056349–109056897 | −0.26 | 4 | opposite | DPPA4 | 219,259 |
| 6 | ATRX | 34499314–34499504 | −0.28 | 4 | Sotos | 34499314–34499504 | −0.17 | 4 | same | PACSIN1 | 0 |
| 16 | ATRX | 58019866–58019984 | −0.37 | 3 | Sotos | 58019866–58019984 | −0.27 | 3 | same | TEPP | 0 |
| 10 | ATRX | 43698834–43699070 | −0.33 | 3 | Sotos | 43698834–43699070 | −0.32 | 3 | same | RASGEF1A | 656 |
| 18 | ATRX | 77905119–77905751 | −0.18 | 10 | Sotos | 77905663–77905751 | 0.16 | 4 | opposite | PARD6G-AS1 (56bp away) | 0 |
| 1 | ATRX | 228291486–228291705 | 0.23 | 5 | Sotos | 228291591–228291682 | 0.18 | 3 | same | – | 301 |
| 18 | ATRX | 74499372–74499584 | 0.2 | 5 | Sotos | 74499372–74499584 | −0.17 | 5 | opposite | – | 0 |
| 1 | ATRX | 3634867–3635100 | −0.22 | 4 | Sotos | 3634867–3635100 | −0.2 | 4 | same | TP73 | 0 |
| 7 | GTPTS | 27182493–27185282 | −0.36 | 51 | Kabuki | 27182493–27183816 | 0.15 | 18 | opposite | HOXA5 | 0 |
| 7 | GTPTS | 27182493–27185282 | −0.36 | 51 | CHARGE | 27182493–27183946 | 0.23 | 20 | opposite | HOXA5 | 0 |
| 14 | GTPTS | 54418728–54418851 | −0.38 | 3 | SBBYSS | 54418728–54418851 | −0.2 | 3 | same | BMP4 | 0 |