We found that 9 HLA classical alleles (HLA-DRB1: *11:04, *08:01, *07:01, *13:01, *11:03 and HLA-DBP1: *13:01, *26:01, *40:01, *06:01) together with 16 expression-model-derived independent C4 eQTLs can explain almost all associations of SSc with the MHC region (Supplementary Fig. 5B). Here, C4A is linked to systemic sclerosis.