Recent large-scale genetic approaches such as genome-wide association studies have allowed the identification of common geneticvariations that contribute to risk architectures of psychiatric disorders. However, most of these susceptibility variants are located innoncoding genomic regions that usually span multiple genes. As a result, pinpointing the precise variant(s) and biological mechanismsaccounting for the risk remains challenging. By reviewing recent progresses in genetics, functional genomics and neurobiology ofpsychiatric disorders, as well as gene expression analyses of brain tissues, here we propose a roadmap to characterize the roles ofnoncoding risk loci in the pathogenesis of psychiatric illnesses (that is, identifying the underlying molecular mechanisms explaining thegenetic risk conferred by those genomic loci, and recognizing putative functional causative variants). This roadmap involves integration of transcriptomic data, epidemiological and bioinformatic methods, as well as in vitro and in vivo experimental approaches. These tools will promote the translation of genetic discoveries to physiological mechanisms, and ultimately guide the development of preventive, therapeutic and prognostic measures for psychiatric disorders.