Notable disease relevant associations include IFN-γ specific transcript QTL at COVID-19 severity locus rs10735079, where allelic variation modulates context-specific splicing of OAS1, and at rs4072037, a risk allele for gastro-esophageal cancer, which associates with context-specific splicing of MUC1. We use DNA methylation data from the same cells to demonstrate overlap between methylation QTL and causal context-specific expression QTL, permitting inference of the direction of effect. Here, IFNG is linked to COVID-19.