We identified a total of 4,858 significant differential interactions (weighted adjusted P < 0.05) between SSc patients and healthy controls in CD4+ T cells originating from 1,526 captured promoters, although the significance was modest (median weighted adjusted P = 2.2 × 10−2) as compared with differential interactions between cell types (median weighted adjusted P = 2.16 × 10−10). Here, CD4 is linked to systemic sclerosis.