We found that there was a large difference in association patterns between the diffuse forms of SSc (dcSSc and ATA-positive SSc) and the limited forms of SSc (lcSSc and ACA-positive SSc); the solely strong association of the HLA locus was identified in the diffuse forms of SSc, while the associations of HLA was much weaker and multiple loci outside the HLA region including STAT4 locus were associated with the limited forms of SSc (Fig. 5a, Supplementary Fig. 9, Supplementary Data 19). Here, STAT4 is linked to systemic sclerosis.