Table 1 Summary of DMR’s identified in the analysis of FAP versus healthy colon organoids that overlapped with CRC GWAS SNPs
Genomic position (Number of CpGs in region) | P | FDR | Mean difference (Beta) | Overlapping genes | SNP |
|---|---|---|---|---|---|
chr13: 78492568–78494462 [41] | 4.90E−21 | 9.43E−19 |  − 0.117 | RNF219-AS1, EDNRB | rs1330889 |
chr5: 135415190–135416613 [16] | 3.48E−20 | 4.46E−18 |  − 0.246 | VTRNA2-1 | rs4976270 |
chr13: 36871646–36872346 [12] | 4.47E−15 | 2.15E−13 | 0.135 | SOHLH2, CCDC169-SOHLH2, CCDC169 | rs7333607 |
chr10: 50602990–50604518 [14] | 4.75E−10 | 8.70E−09 |  − 0.085 | DRGX | rs10821907 |
chr16: 68676451–68677364 [8] | 1.24E−09 | 2.08E−08 | 0.123 | CDH3 | rs9924886 |
chr6: 31894831–31895598 [9] | 2.04E−09 | 3.27E−08 |  − 0.105 | C2, CFB | rs2516420, rs3830041 |
chr10: 102821427–102822249 [9] | 2.05E−08 | 2.25E−07 |  − 0.086 | KAZALD1 | rs4919687 |
chr12: 50614713–50616779 [9] | 5.49E−07 | 3.77E−06 |  − 0.093 | RP3-405J10.4, LIMA1 | rs12372718 |
chr12: 115124584–115126061 [8] | 7.46E−06 | 3.26E−05 |  − 0.136 | NA | rs7300312 |
chr5: 126408756–126410348 [14] | 8.17E−05 | 2.35E−04 |  − 0.142 | C5orf63 | rs12659017 |
chr6: 32115979–32116963 [19] | 9.69E−05 | 2.70E−04 |  − 0.083 | PRRT1 | rs3830041, rs2516420 |
chr1: 109849705–109850837 [8] | 1.50E−04 | 3.94E−04 |  − 0.072 | NA | rs2938616 |
chr6: 35108605–35109398 [12] | 3.73E−04 | 8.08E−04 | 0.066 | TCP11 | rs16878812 |
chr10: 99734513–99735202 [7] | 4.99E−04 | 1.04E−03 | 0.080 | CRTAC1 | rs10786560, rs11190164 |
chr6: 29795595–29796614 [11] | 7.37E−04 | 1.40E−03 | 0.108 | HLA-G, HCG4P8 | rs1476570 |
chr15: 67390372–67391147 [7] | 7.42E−04 | 1.40E−03 |  − 0.132 | SMAD3 | rs56324967, rs745213 |
chr6: 30079139–30079662 [13] | 7.61E−04 | 1.42E−03 |  − 0.135 | TRIM31-AS1, TRIM31 | rs3131043 |
chr3: 113160071–113160821 [13] | 2.76E−03 | 4.25E−03 | 0.051 | WDR52 | rs13086367, rs12635946, rs72942485 |
chr12: 50297581–50298198 [7] | 2.81E−03 | 4.32E−03 | 0.064 | FAIM2 | rs12372718 |
chr19: 58446600–58446988 [10] | 2.92E−03 | 4.45E−03 |  − 0.073 | ZNF418 | rs73068325 |
chr12: 95945082–95945927 [10] | 4.76E−03 | 6.76E−03 |  − 0.069 | USP44 | rs11108175 |
chr6: 31276088–31276797 [13] | 6.61E−03 | 8.93E−03 |  − 0.065 | XXbac-BPG248L24.10 | rs3131043, rs116353863, rs116685461 |
chr20: 62795464–62796178 [9] | 8.16E−03 | 0.011 |  − 0.073 | MYT1 | rs1741640 |
chr11: 101454317–101454996 [12] | 9.46E−03 | 0.012 | 0.106 | TRPC6 | rs2186607 |
chr6: 31733889–31734232 [9] | 0.016 | 0.020 | 0.073 | VWA7 | rs116685461, rs2516420 |
chr11: 111385338–111385778 [7] | 0.026 | 0.029 |  − 0.070 | C11orf88, RP11-794P6.6 | rs3087967 |
chr5: 134914923–134915088 [7] | 0.038 | 0.042 |  − 0.074 | CTC-321K16.1, CXCL14 | rs4976270 |