First, enrichment was investigated using a hypergeometric test (as previously described39) using SNPs from the GWAS Catalog (hg19, downloaded 02/11/2015) as background. The GWAS Catalog was pruned within each contributing GWAS study to retain only SNPs that were at least 1Mb apart within that study resulting in 18,202 SNPs for further analysis. BEDtools was used to calculate overlap with precomputed “gapped peaks” for H3K4me1 and H3K4me3 histone marks and a hypergeometric test was used to test the significance of enrichment of the 97 lung function variants compared to the background of GWAS Catalog SNPs. Control for multiple testing was undertaken by picking 97 random variants from the pruned GWAS Catalog and repeating the enrichment computation. FDR was calculated from 10,000 randomizations and FDR=10% was used as a threshold.
