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To date, JIA genetic association studies have had limited sample sizes, used\u00a0heterogeneous patient populations, or included only candidate regions. The aim of this study was to identify new associations between JIA patients with oligoarticular disease and those with IgM rheumatoid factor (RF)\u2212negative polyarticular disease, which are clinically similar and the most prevalent JIA disease subtypes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Three cohorts comprising 2,751 patients with oligoarticular or RF\u2010negative polyarticular JIA were genotyped using the Affymetrix Genome\u2010Wide SNP Array 6.0 or the Illumina HumanCoreExome\u201012+ Array. Overall, 15,886 local and out\u2010of\u2010study controls, typed on these platforms or the Illumina HumanOmni2.5, were used for\u00a0association analyses. High\u2010quality single\u2010nucleotide polymorphisms (SNPs) were used for imputation to 1000 Genomes prior to SNP association analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Meta\u2010analysis showed evidence of association (<jats:italic>P<\/jats:italic> &lt; 1 \u00d7 10<jats:sup>\u22126<\/jats:sup>) at 9 regions: <jats:italic>PRR9<\/jats:italic>_<jats:italic>LOR<\/jats:italic> (<jats:italic>P<\/jats:italic> = 5.12 \u00d7 10<jats:sup>\u22128<\/jats:sup>), <jats:italic>ILDR1<\/jats:italic>_<jats:italic>CD86<\/jats:italic> (<jats:italic>P<\/jats:italic> = 6.73 \u00d7 10<jats:sup>\u22128<\/jats:sup>), <jats:italic>WDFY4<\/jats:italic> (<jats:italic>P<\/jats:italic> = 1.79 \u00d7 10<jats:sup>\u22127<\/jats:sup>), <jats:italic>PTH1R<\/jats:italic> (<jats:italic>P<\/jats:italic> = 1.87 \u00d7 10<jats:sup>\u22127<\/jats:sup>), <jats:italic>RNF215<\/jats:italic> (<jats:italic>P<\/jats:italic> = 3.09 \u00d7 10<jats:sup>\u22127<\/jats:sup>), <jats:italic>AHI1<\/jats:italic>_<jats:italic>LINC00271<\/jats:italic> (<jats:italic>P<\/jats:italic> = 3.48 \u00d7 10<jats:sup>\u22127<\/jats:sup>), <jats:italic>JAK1<\/jats:italic> (<jats:italic>P<\/jats:italic> = 4.18 \u00d7 10<jats:sup>\u22127<\/jats:sup>), <jats:italic>LINC00951<\/jats:italic> (<jats:italic>P<\/jats:italic> = 5.80 \u00d7 10<jats:sup>\u22127<\/jats:sup>), and <jats:italic>HBP1<\/jats:italic> (<jats:italic>P<\/jats:italic> = 7.29 \u00d7 10<jats:sup>\u22127<\/jats:sup>). Of these, <jats:italic>PRR9_LOR, ILDR1_CD86, RNF215, LINC00951,<\/jats:italic> and <jats:italic>HBP1<\/jats:italic> were shown, for the first time, to be autoimmune disease susceptibility loci. Furthermore, associated SNPs included <jats:italic>cis<\/jats:italic> expression quantitative trait loci for <jats:italic>WDFY4<\/jats:italic>,<jats:italic> CCDC12<\/jats:italic>,<jats:italic> MTP18<\/jats:italic>,<jats:italic> SF3A1<\/jats:italic>,<jats:italic> AHI1<\/jats:italic>,<jats:italic> COG5<\/jats:italic>,<jats:italic> HBP1<\/jats:italic>, and <jats:italic>GPR22<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>This study provides evidence of both unique JIA risk loci and risk loci overlapping between JIA and other autoimmune diseases. These newly associated SNPs are shown to influence gene expression, and their bounding regions tie into molecular pathways of immunologic relevance. Thus, they likely represent regions that contribute to the pathology of oligoarticular JIA and RF\u2010negative polyarticular JIA.<\/jats:p><\/jats:sec>","DOI":"10.1002\/art.40216","type":"journal-article","created":{"date-parts":[[2017,7,18]],"date-time":"2017-07-18T12:12:59Z","timestamp":1500379979000},"page":"2222-2232","source":"Crossref","is-referenced-by-count":81,"title":["Genome\u2010Wide Association Meta\u2010Analysis Reveals Novel Juvenile Idiopathic Arthritis Susceptibility Loci"],"prefix":"10.1002","volume":"69","author":[{"given":"Laura A.","family":"McIntosh","sequence":"first","affiliation":[{"name":"Cincinnati Children's Hospital Medical Center and University of Cincinnati Cincinnati Ohio"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miranda C.","family":"Marion","sequence":"additional","affiliation":[{"name":"Wake Forest University School of Medicine Winston\u2010Salem North Carolina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Sudman","sequence":"additional","affiliation":[{"name":"Cincinnati Children's Hospital Medical Center Cincinnati Ohio"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary E.","family":"Comeau","sequence":"additional","affiliation":[{"name":"Wake Forest University School of Medicine Winston\u2010Salem North Carolina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mara L.","family":"Becker","sequence":"additional","affiliation":[{"name":"Children's Mercy\u2010Kansas City Kansas City Missouri"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John F.","family":"Bohnsack","sequence":"additional","affiliation":[{"name":"University of Utah Salt Lake City"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tasha E.","family":"Fingerlin","sequence":"additional","affiliation":[{"name":"National Jewish Health and University of Colorado Denver"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas A.","family":"Griffin","sequence":"additional","affiliation":[{"name":"Levine Children's Specialty Center Charlotte North Carolina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. 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