Annotation and functional relevance
Significant CpG sites were annotated by GREAT v3.0.017. We correlated the significant CpG sites we identified to the expression level of gene nearby (with a region of +/- 250kb) by cis expression quantitative trait DNA methylation (cis -eQTM) analysis. Blood eQTM was assessed in the BIOS consortium dataset18. Matched nasal RNA sequencing data and DNA methylation data was used to perform eQTM analysis for significant nasal CpG sites and these results were additionally replicated in the larger collection of nasal brushes obtained in the PIAMA study19. The genes that were identified in eQTM analysis were used for pathway analysis by ConsensusPathDB20. To check if the results of replicated CpG sites were affected by inhaled corticosteroids (ICS), we stratified asthma subjects by ICS usage, and compared the DNA-methylation in the remission group to asthma with ICS and asthma without ICS group, respectively, by t-test.