Results for the causal inference test (CIT) in CD4+ T cells and B cells as reported in Table II of Clark et al. [33] when any nominal p-value was less than 0.05 (but focussing on those triplets also satisfying the CIT permutation false-discovery rate (FDR) threshold of 0.05, so effectively providing an adjustment for multiple testing).

When there are multiple gene expression probes for the same SNP and methylation, the most statistically significant probe was reported. Here along with the CIT p-value and CIT permutation FDR, we report the results from the BN analyses of the same data triplets with no imputation (specifically, the direction, strength and edge probabilities as calculated from the average best-fitting network).