The data presented in this article are related to the research article entitled “A critical role of transcription factor YY1 in rheumatoid arthritis by regulation of interleukin-6” (J. Lin, Y. He, J. Chen, Z. Zeng, B. Yang, Q. Ou, 2016) [1]. The article describes YY1 overexpression is specific for RA, but not for SLE, SS, DM or MCTD. In early RA, YY1 expression is also increased. In asymptomatic subjects with RF or ACPA positive who have high risk for developing RA, the YY1 expression is not increased obviously. Moreover, YY1 expression is positively correlated with serum CRP or ESR. In RA patients treated with anti-IL-6R monoclonal Ab tocilizumab, there is no significant difference in YY1 expression after IL-6 blocking therapy.