Although rs2476601 was not significantly associated with SLE (P = 0.20) in HS, this SNP was marginally significant with anti-nRNP positive SLE cases (P = 0.037, OR = 1.99; 108 cases positive, 229 cases negative) in case-only analysis ( Table 2 ). For anti-nRNP positive cases versus healthy controls association remained significant (P = 0.002, OR = 1.90). MAF of the ‘A’ allele increased from 4.6% in controls to 8.3% in anti-nRNP positive cases. SNP rs3765598 was associated with malar rash (P = 0.003, OR = 1.91; 316 cases positive, 169 cases negative) but this result was not confirmed in case positive vs. controls (P = 0.61, OR = 0.95). While neither of the case-only results were significant after adjusting for FDR (PnRNP-rs2476601 = 0.88, Pmalar-rs3765598 = 0.68), the sample sizes for these analyses were quite small and lacked statistical power. Notable, SLE cases negative for malar rash had the lowest MAF (MAFCONTROL = 16.8%, MAFNEG = 8.6%, MAFPOS = 15.2).
