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Background  Schizophrenia is a severe mental disease with high morbidity and heritability. The  SLC39A8  gene is located in 4q24 and encodes a protein that transports many metal ions. Multiple previous studies found that one of the most pleiotropic single nucleotide polymorphisms (SNPs) in  SLC39A8 , rs13107325, is associated with schizophrenia in the European population. However, the polymorphism of this locus is rare in other populations. In China, the Han Chinese and the Uygur Chinese are two ethnic populations that originate from different races.    Methods  A case-control study was conducted with 983 schizophrenia cases and 1230 healthy controls of the Chinese Uygur population. To validate the most promising SNP, meta-analyses were conducted with the Han Chinese and the European PGC2 data sets reported previously.    Results  A susceptible locus, rs10014145 ( p  allele  = 0.014,  p  allele  = 0.098 after correction;  p  genotype  = 0.004,  p  genotype  = 0.032 after correction) was identified in case-control study of the Chinese Uygur population. Further, the association between rs10014145 and schizophrenia was supported by a meta-analysis of Han and Uygur Chinese samples (pooled OR [95% CI] =1.10 [1.03–1.17], Z = 2.73,  p  = 0.006). The association between rs10014145 and schizophrenia was not significant in a meta-analysis of combined Chinese and European samples (pooled OR [95% CI] =1.07 [1.00–1.14], Z = 1.88, and  p  = 0.06). In addition, the “CCAC” haplotype of rs4698844-rs233814-rs13114343-rs151394 was significantly associated with schizophrenia in Uygur Chinese ( P  = 0.003, corrected  p  = 0.012).    Conclusions  The results of this study support that  SLC39A8  is a susceptible gene for schizophrenia in the populations of Han Chinese and Uygur Chinese in China, further studies are suggested to validate the association.    Electronic supplementary material  The online version of this article (10.1186/s12888-019-2240-2) contains supplementary material, which is available to authorized users.

SLC39A8 is a risk factor for schizophrenia in Uygur Chinese: a case-control study