To assess whether PTPN22 genetic associations were enriched in SLE patients with specific clinical manifestations, a case-only analysis of the 11 ACR classification criteria and 5 autoantibodies was performed. Case-only analysis demonstrated association between rs2476601 and anticardiolipin IgG (aCL IgG >20) antibody using 121 patients positive compared to 578 SLE patients known to be negative for aCL IgG (P = 0.012, OR = 1.65 (95%CI = 1.11–2.46)) ( Table 2 ). When adjusting for false discovery rate (FDR) this association remained significant, though the association was modest (FDR = 0.049). The allelic effect (OR) increased when these EA cases were compared to 3491 EA controls (P = 8.43×10−5, OR = 2.07, 95%CI = 1.42–2.99; FDR = 0.0008). The effect was further increased using 56 EA patients with high titer aCL IgG>40 (P = 9.67×10−6, OR = 2.79 95%CI 1.73–4.48; FDR = 9.67×10−5). The MAF of the ‘A’ allele increased from 8% in controls to 11% in all SLE cases, 15% in cases positive for aCL IgG, and 20% in cases with aCL IgG>40. Additional analyses suggest a positive correlation between
