These include sites with evidence of altered methylation in protein-coding, lncRNA, and pseudogenes and concomitant differential expression in MGC12916, DLX5, and TMEM140. Although this cross-sectional study cannot separate causality from response to disease, it identifies DNA methylation alterations in genes and pathways that are important in SSc, showing that distinct DNA methylation changes underlie SSc in African Americans. Here, ENSG00000266709 is linked to systemic sclerosis.