Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieved significant reduction in our variant search space and nominated candidate variants predicted to regulate known CCDD disease genes <i>MAFB, PHOX2A, CHN1</i>, and <i>EBF3</i> - as well as new candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. Here, PHOX2A is linked to atrial conduction disease.