Among the SNPs, NCF1 SNP rs201802880 showed the strongest associations with susceptibility to SLE and SSc (SLE: uncorrected P value [Puncorr] = 3.77 × 10−44, FDR P value [Q] = 8.29 × 10−43, Odds Ratio [OR] = 3.57, 95%CI 2.99-4.28; SSc: Puncorr = 2.40 × 10−4, Q = 0.0011, OR = 1.50, 95%CI 1.21–1.87, both under the additive model). Here, NCF1 is linked to systemic sclerosis.