Concerning the relationships of the studied SNPs with clinical features of SLE, CT + TT of MECP2 rs2734647 was correlated with elevated ACR, higher SLEDAI, and therapeutic drugs, while CT + TT of TIRAP rs8177374 was correlated with elevated ACR, higher ESR, and therapeutic drugs in nephritis patients, which may contribute to disease severity and progression, and could be linked with SLE prognosis. Here, MECP2 is linked to nephritis.