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•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...
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