Table 2. CpG sets considered in this analysis.

CpG set	Number of CpGs	Notes
Array background	391,814	Intersection of CpGs on Illumina HM450 (ENID 2 yr) and EPIC (EMPHASIS) cohort arrays, post QC
SoC-CpGs	259	SoC-associated CpGs with SoC effect size (SoC methylation amplitude) > 4% in the ENID 2 yr dataset
Matched controls	259	CpGs with similar methylation distributions to SoC-CpGs in the ENID 2 yr dataset*
Random controls	259	Random sample from array background

^*Matching methylation distributions determined by Kolmogorov-Smirnov tests (see Appendix 1—figure 16). QC: quality control; LRT: likelihood ratio test. See Materials and methods for further details.