Inflammatory bowel disease (IBD) has a wide range of risk factors including genetics, environment and gut microbiota. The pathology of the disease still remains unclear. This thesis is mainly based on the studies from 1000IBD cohort of University Medical Center Groningen, describing how genetics regulate gene expressions, protein levels, metabolites, gut microbiota and how these interactions are related to IBD. By using omics data integration approach, I revealed novel biological pathways potentially involved in the disease onset, which could provide new strategies in clinical practice