In summary, taking advantage of our GWAS data and a large replication cohort, we have identified three new non-HLA loci associated with subphenotypes of SSc: GRB10, IRF8, and SOX5. In addition, we shed light on HLA associations with this disease, establishing different patterns of independent association in the ACA and ATA positive subgroups. This evidence concerns the gene GRB10 and systemic sclerosis.