Results of Simple Sum colocalization and contrasting colocalization analyses for the three meconium ileus genome-wide significant loci, and colocalization posterior probabilities from COLOC and eCAVIAR.

The eQTL evidence is the GTEx p-value based on the -log10(eQTL p) scale for a specified gene and tissue. The meconium ileus-SNP association evidence is the -distributed Wald test statistic obtained in this study. Analytical (and permutation-based) Simple Sum (SS) colocalization p-values correspond to each individual tissue and evaluates if the eQTLs and meconium ileus-associated variants colocalize. Simple Sum contrasting (SSC) colocalization p-value evaluates if the eQTLs in the pancreas colocalize with meconium ileus-associated variants more than eQTLs in another tissue; NAs are listed for the pancreas since we do not contrast pancreas with itself. All p-values are one-sided because only positive association implies eQTL-association colocalization (i.e. eQTL peaks coincide with association peaks). COLOC [43] PP represents the posterior probability of eQTL-association colocalization calculated for each individual tissue. eCAVIAR [44] calculates SNP-level colocalization posterior probability (CLPP) for each variant in a locus for a given gene and in a given tissue. The regional colocalization probability (RCP) can be defined by summation of the SNP-level CLPP in a given LD block; RCP is recommended in [49] and the results are provided in the ‘eCAVIAR RCP’ column. eCAVIAR maximum regional CLPP provides similar qualitative results as eCAVIAR RCP thus are not shown here.