Disrupted neuronal function in schizophrenia is unlikely to be restricted to the synapse, but the concentration of associations in genes with pre- and post-synaptic locations, and with functions related to synaptic organisation, differentiation and transmission, point to the pathophysiological importance of these neuronal compartments and their attendant functions. This is further supported by studies showing substantial effects on schizophrenia risk of CNVs39 and rare damaging coding variants in genes with similar functions, including some of the same genes (SCHEMA; companion paper). Genomic studies, therefore, converge in highlighting these areas of biology as targets for research aiming for a mechanistic understanding of the disorder; the large number of prioritised genes and variants identified here offer an unprecedented empirically-supported resource for that endeavour.