Here we integrate differential expression and expression quantitative trait locus (eQTL) analyses in monocyte-derived macrophages (MDMs) from patients with SSc and healthy controls, revealing (1) changes in macrophage transcriptome as an important contributor to SSc and (2) upregulation and cis-regulation of GSDMA (a candidate gene for SSc susceptibility) contributing to disease risk in macrophages but not in skin. The gene discussed is GSDMA; the disease is systemic sclerosis.