Table 2.
Analysis of variants within CpG islands & shores (MAF ≤ 5%)
| CpG Island & Shores | Nearest Gene | Probe | nVars | P-value |
|---|---|---|---|---|
| chr21:45,728,220–45,732,444 | PFKL | cg21069494 | 6 | 6.24x10−24 |
| chr8:144,715,866–144,720,798 | ZNF623 | cg16316162 | 3 | 4.02x10−23 |
| chr11:66,492,937–66,498,387 | SPTBN2 | cg24851651 | 6 | 2.68x10−21 |
| chr2:75,785,717–75,790,312 | EVA1A | cg26175789 | 8 | 6.73x10−21 |
| chr12:120,753,346–120,757,672 | PLA2G1B | cg06379361 | 5 | 1.21x10−20 |
| chr7:100,873,555–100,878,212 | CLDN15 | cg01299997 | 7 | 1.26x10−20 |
| chr3:53,076,956–53,083,101 | RFT1 | cg04865290 | 10 | 2.03x10−20 |
| chr2:196,519,555–196,524,950 | SLC39A10 | cg19655195 | 8 | 2.23x10−20 |
| chr1:1,287,707–1,293,126 | MXRA8 | cg17132079 | 3 | 1.11x10−19 |
| chr11:64,407,877–64,413,253 | NRXN2 | cg19395706 | 4 | 1.43x10−19 |
Top 10 results for analysis between low frequency variants collapsed within CpG Island & flanking Shore regions (where there is no previously reported single variant mQTL effect) and nearby methylation probe (+/- 1Mb of region analysed). nVars = number of variants analysed. Probe = 450k probe ID. P-value = P-value according to SKAT.