RUNX3 gene polymorphisms are associated with clinical features of systemic lupus erythematosus in Chinese Han population

•Three SNPs (rs7536201, rs4649038, rs11249215) in or around RUNX3 gene were genotyped in Han Chinese population.•Malar rash, discoid rash and Neurological disorder were shown association with the T allele of rs4649038.•RUNX3 might be a common susceptibility gene shared by SLE and psoriasis as well as ankylosing spondylitis.•RUNX3 is associated with different phenotypes of SLE and might contribute to the complexity of SLE clinical features.