Common genetic variants explain a significant proportion of the genetic risk in autism or conduct disorder. However, it is unclear to what extent these variants also influence the expression of disorder associates phenotypes and which biological networks are particularly relevant. In this genome-wide study, we test common single nucleotide polymorphisms for association with clinical measures and identify the underlying genes. Bioinformatic and graph-theoretical analyses enable us to identify specific processes. Here we also draw on our cohort of families and affected individuals, which is unique in Germany. We also emphasise the many years of close collaboration with patients, relatives and clinics. The analysis and validation of the results are carried out in data from the Autism Genome Project and the SFARI Autism Initiative as well as the FemNAT/CD study.