Significance A fundamental question of neuroscience is how the brain wires itself. Here, we propose a modeling framework that explains how cellular connectivity emerges from neuronal identity, allowing us to offer experimentally falsifiable predictions on the genetic encoding of the connectome. The rapid advances in brain science require quantitative frameworks to integrate genetic and connectome information. The proposed model responds to this need, helping us unveil the genetically driven mechanisms that govern the formation of individual links in the brain.