Here, we undertook a characterization of the chromatin accessibility and gene expression profiles of CD4 T cells to assess their contribution to inflammation of the gut and showed that IBD risk loci are linked to Th17 cells and that a pTh17 cell subpopulation co-expressing Th1 and cytotoxic gene programs is associated with intestinal inflammation in IBD patients. Here, CD4 is linked to inflammatory bowel disease.