We also found that EA lupus patients with co-existent thyroid disease strengthened the observed association result. The OR for SNP rs2476601 was increased to OR = 2.07 (95%CI 1.44–2.99), when 117 European cases with co-existent thyroid disease were compared with 3491 European controls with a MAF of 15% in cases in compare to 8% in controls (P = 6.38×10−5; FDR = 0.001). Among these, only 24 (20%) had aCL IgG>20 and in a separate analysis, lupus patients with co-existent thyroid disease and aCL IgG<20 (93 patients) still shows similar increased risk (P = 0.001, OR = 1.94 95%CI 1.27–2.95). In case-only analyses when these cases were compared with 514 SLE patients with no history of thyroid disease a similar trend was obtained (P = 0.02, OR = 1.60, 95%CI = 1.06–2.39).
