AbstractComplex diseases are heterogenous due to variation in their genetic and environmental underpinnings, leading to varied treatment responses. Genome‐wide association studies (GWAS) integrated with single‐cell expression quantitative trait loci analyses (eQTL) can pinpoint cell‐type specific candidate disease‐relevant genes and pathways. This knowledge can be applied to patient stratification and novel therapeutic target identification. Here, we describe the translational potential of cell‐type specific genetic regulation, using Crohn's disease as an example.