The advent of genome wide association studies have resulted in the identification of a number of novel genetic loci for schizophrenia and related disorders. Understanding the functional impact of these variants on brain structure and function is crucial to understand their role in disease pathology. We presents data based on our genetic and neuropsychological assessment of almost 700 patients and healthy participants for a number of these variants and replication of our findings in independent samples of almost 1500 cases and controls. Specifically, we will use this data to suggest that the risk associated with some genetics variants (e.g. NOS1) is being mediated by an influence on variation in intelligence and other cognitive phenotypes, while other risk variants (e.g. ZNF804A) delineate illness subtypes in which cognitive deficits are a less prominent feature.