Abstract: Objective To explore the gene polymorphisms of lnc5150 (ENST00000425150) in association with systemic lupus erythematosus (SLE) in a HAN population. Methods A case-control study was performed by recruiting 658 SLE cases and 843 healthy controls. Two lnc5150 single nucleotide polymorphisms (SNPs) (rs144047453, rs141561256) were genotyped using TaqMan genotyping assays on Fluidigm 192.24 system. The distribution of genotype and allele frequencies of two SNPs were detected, besides those, the genotype effects of dominant and recessive models were also analysed. As well, the association between SNPs and clinical manifestations in SLE patients were analysed. Results No significant differences were detected for the distribution of allele and genotype, and we failed to find any significant results about dominant and recessive models of two SNPs (all P>0.05). However, further analysis in SLE patients revealed that the AA genotypes and A allele of the lnc5150 rs141561256 polymorphism were nominally significantly higher in SLE patients with lupus nephritis (LN) (all P<0.05). Conclusions Lnc5150 SNPs are not associated with genetic susceptibility to SLE, but they might contribute to some clinical phenotype of SLE.