ObjectivesSystemic sclerosis (SSc) is a complex autoimmune disease with a strong genetic component. However, most of the causal genes and variants are still unknown. The challenge in the post-GWAS era is to use functional genomics to translate genetic findings into patients’ benefit, particularly in disease-relevant cell types.MethodsPromoter capture Hi-C (pCHi-C) and RNA sequencing experiments were performed in a total of 30 samples corresponding to CD4+ T cells and CD14+ monocytes (15 samples each) from SSc patients and healthy controls to link SSc-associated variants with their target genes, followed by differential expression and differential interaction analyses between both cell types. We also aimed to identify potential drugs that could be repurposed for its use in SSc.ResultsWe linked SSc-associated loci to 39 new potential target genes, confirming 7 previously assigned genes. We highlight novel causal genes, such as CXCR5 as the most probable candidate gene for the DDX6 locus. Some SSc confirmed genes such as IRF8, STAT4, or CD247 interestingly showed cell type specific interactions. We also identified 15 potential drug targets already in use in other similar immune-mediated diseases that could be repurposed for SSc treatment. Furthermore, we observed that interactions are directly related with the expression of important genes implicated in cell type specific pathways.ConclusionsOur study reveals potential causal genes for SSc-associated loci, some of them acting in a cell type specific manner, suggesting novel biological mechanisms that may mediate SSc pathogenesis.