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Background  Our understanding of the genetic factors underlying juvenile idiopathic arthritis (JIA) is growing, but remains incomplete. Recently, a number of novel genetic loci were reported to be associated with JIA at (or near) genome-wide significance in a large case–control discovery sample using the Immunochip genotyping array. However, independent replication of findings has yet to be performed. We therefore attempted to replicate these newly identified loci in the Australian CLARITY JIA case–control sample.    Findings  Genotyping was successfully performed on a total of 404 JIA cases (mean age 6.4 years, 68% female) and 676 healthy child controls (mean age 7.1 years, 42% female) across 19 SNPs previously associated with JIA. We replicated a significant association (p < 0.05, odds ratio (OR) in a direction consistent with the previous report) for seven loci, six replicated for the first time -  C5orf56-IRF1  (rs4705862),  ERAP2-LNPEP  (rs27290),  PRR5L  (rs4755450),  RUNX1  (rs9979383),  RUNX3  (rs4648881), and  UBE2L3  (rs2266959).    Conclusions  We have carried out the first independent replication of association for six genes implicated in JIA susceptibility. Our data significantly strengthens the evidence that these loci harbor true disease associated variants. Thus, this study makes an important contribution to the growing body of international data that is revealing the genetic risk landscape of JIA.    Electronic supplementary material  The online version of this article (doi:10.1186/1546-0096-12-53) contains supplementary material, which is available to authorized users.

Independent confirmation of juvenile idiopathic arthritis genetic risk loci previously identified by immunochip array analysis