TABLE 6.
Differentially methylated regions identified in candidate genes.
| Chr | Start | End# CpG | Delta methylation | Gene | distance to TSS | Genomic feature* | Candidate group& |
| MZ11 | 2976318 | 297910310 | 0.50 | PRDM16 | −8 | IGR | MGI |
| 1 | 55359014 | 553591535 | −0.51 | DHCR24 | −6 | IGR | SCLP |
| 1 | 93425751 | 934258035 | 0.50 | RPL5 | 128 | In | SCLP |
| 1 | 243451450 | 2434515444 | −0.53 | SDCCAG8 | 32 | In | MGI |
| 2 | 114099657 | 1141003026 | −0.59 | PAX8 | −63 | IGR | AGV |
| 3 | 13787881 | 137879714 | −0.78 | WNT7A | 134 | IGR | AGV |
| 3 | 41282685 | 412832684 | −0.52 | CTNNB1 | 42 | IGR | AGV |
| 3 | 129328813 | 1293291188 | 0.54 | PLXND1 | −3 | IGR | MGI |
| 3 | 189509045 | 1895095354 | 0.58 | TP63 | 160 | In | AGV |
| 5 | 149861203 | 1498614154 | −0.51 | NDST1 | −26 | IGR | MGI |
| 8 | 96365815 | 963658694 | 0.85 | GDF6 | 807 | IGR | SCLP |
| 10 | 131555549 | 1315558496 | −0.51 | MGMT | 290 | In | AGV |
| 12 | 99652840 | 996528965 | 0.54 | APAF1 | 614 | In | MGI |
| 12 | 125008438 | 1250117835 | 0.55 | NCOR2 | 30 | In | SCLP |
| 13 | 106929698 | 1069302854 | 0.55 | EFNB2 | 257 | IGR | MGI |
| 14 | 37123643 | 371237005 | −0.62 | PAX9 | −7 | IGR | MGI |
| 14 | 53976736 | 539769235 | 0.64 | BMP4 | 447 | IGR | AGV |
| 15 | 26877653 | 268778594 | 0.54 | GABRB3 | 140 | In | MGI |
| 16 | 79361536 | 793616375 | 0.60 | MAF | 273 | IGR | AGV |
| 17 | 42646731 | 426467965 | −0.66 | FZD2 | 12 | IGR | MGI |
| 17 | 72038593 | 720406385 | 0.53 | RPL38 | −160 | IGR | MGI |
| 18 | 46345407 | 463455535 | 0.52 | SMAD7 | 132 | In | MGI |
| 22 | 34207931 | 342113294 | −0.50 | LARGE | 107 | In | AGV |
| MZ21 | 87668656 | 876687255 | −0.63 | HS2ST1 | 288 | IGR | MGI |
| 1 | 164904923 | 1649049784 | −0.54 | PBX1 | 376 | IGR | AGV |
| 3 | 57741006 | 577431715 | 0.50 | SLMAP | 0 | Prom | MGI |
| 4 | 157863234 | 1578633284 | −0.55 | PDGFC | 29 | In | AGV |
| 6 | 44424513 | 444245704 | −0.54 | RUNX2 | −872 | IGR | MGI |
| 14 | 29568885 | 295695974 | −0.56 | FOXG1 | 334 | IGR | SCLP |
| MZ32 | 145216430 | 1452167095 | −0.58 | ZEB2 | 62 | In | MGI |
| 5 | 176551269 | 1765513574 | −0.52 | NSD1 | −10 | IGR | SCLP |
| 9 | 17005412 | 170055224 | 0.58 | BNC2 | −135 | IGR | MGI |
| 16 | 4000600 | 40006524 | 0.54 | CREBBP/ADCY9 | −70/166 | IGR | AGV |
| 16 | 85033868 | 850339244 | 0.73 | CRISPLD2 | 180 | In | AGV |
| 17 | 44918054 | 449198024 | −0.53 | WNT3/WNT9B | −23/−10 | IGR | AGV |
| 22 | 19825520 | 198256366 | −0.62 | TBX1 | 81 | In | AGV |
| 22 | 46438139 | 464382034 | 0.51 | WNT7B | −65 | IGR | AGV |
| MZ61 | 156095505 | 1560956085 | 0.63 | LMNA | 11 | In | MGI |
| 2 | 43859116 | 438592215 | 0.52 | THADA | −36 | IGR | AGV |
| 9 | 129250270 | 1292503326 | −0.57 | LMX1B | −126 | IGR | SCLP |
| 11 | 61143440 | 611435494 | 0.56 | TMEM216 | −16 | IGR | SCLP |
| 15 | 28338841 | 283388985 | 0.50 | OCA2 | 6 | In | MGI |
| 20 | 39319752 | 393209396 | −0.68 | MAFB | −2 | Prom | AGV |
| MZ713 | 22473353 | 224734475 | 0.51 | FGF9 | 228 | IGR | MGI |
| 2 | 158607860 | 1586080196 | 0.55 | ACVR1 | 124 | In | MGI |
| 21 | 43048389 | 430485686 | 0.50 | RIPK4 | 139 | IGR | SCLP |
| MZ820 | 39320842 | 393210114 | −0.59 | MAFB | −3 | IGR | AGV |
| 17 | 8869579 | 88696508 | −0.51 | PIK3R5 | −1 | Prom | AGV |
| 16 | 68829893 | 688299584 | 0.51 | CDH1 | 59 | In | AGV |
| 2 | 145247233 | 1452472934 | 0.60 | ZEB2 | 31 | In | MGI |
TSS, transcriptional start site; Genome assembly, GRCh37/hg19; *In, Intron; IGR, intergenic region; Prom, promoter; &AGV, associated genetic variant; SCLP, syndromic cleft lip and palate; MGI, Mouse Genome Informatics (orofacial cleft phenotype).