Together with the identification of PRSS1 as a meconium ileus modifier, the integration of GTEx eQTL evidence and meconium ileus susceptibility associations through colocalization analysis support that variation at the identified modifier loci may reflect SLC6A14, SLC26A9 and ATP12A gene expression, and in the CF pancreas rather than in the intestine or any other meconium ileus-relevant tissues tested. Here, ATP12A is linked to intestinal obstruction in the newborn due to guanylate cyclase 2C deficiency.