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To better understand the genetic basis of the MHC susceptibility loci, we genotyped 7,264 MHC SNPs in 22,647 AS cases and controls of European descent. We impute SNPs, classical HLA alleles and amino-acid residues within HLA proteins, and tested these for association to AS status. Here we show that in addition to effects due to <jats:italic>HLA-B*27<\/jats:italic> alleles, several other <jats:italic>HLA-B<\/jats:italic> alleles also affect susceptibility. After controlling for the associated haplotypes in <jats:italic>HLA-B<\/jats:italic>, we observe independent associations with variants in the <jats:italic>HLA-A<\/jats:italic>, <jats:italic>HLA-DPB1<\/jats:italic> and <jats:italic>HLA-DRB1<\/jats:italic> loci. We also demonstrate that the <jats:italic>ERAP1<\/jats:italic> SNP rs30187 association is not restricted only to carriers of <jats:italic>HLA-B*27<\/jats:italic> but also found in <jats:italic>HLA-B*40:01<\/jats:italic> carriers independently of HLA-B*27 genotype.<\/jats:p>","DOI":"10.1038\/ncomms8146","type":"journal-article","created":{"date-parts":[[2015,5,21]],"date-time":"2015-05-21T10:18:06Z","timestamp":1432203486000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":255,"title":["Major histocompatibility complex associations of ankylosing spondylitis are complex and involve further epistasis with ERAP1"],"prefix":"10.1038","volume":"6","author":[{"given":"Adrian","family":"Cortes","sequence":"first","affiliation":[]},{"given":"Sara L.","family":"Pulit","sequence":"additional","affiliation":[]},{"given":"Paul J.","family":"Leo","sequence":"additional","affiliation":[]},{"given":"Jenny J.","family":"Pointon","sequence":"additional","affiliation":[]},{"given":"Philip C.","family":"Robinson","sequence":"additional","affiliation":[]},{"given":"Michael H.","family":"Weisman","sequence":"additional","affiliation":[]},{"given":"Michael","family":"Ward","sequence":"additional","affiliation":[]},{"given":"Lianne S.","family":"Gensler","sequence":"additional","affiliation":[]},{"given":"Xiaodong","family":"Zhou","sequence":"additional","affiliation":[]},{"given":"Henri-Jean","family":"Garchon","sequence":"additional","affiliation":[]},{"given":"Gilles","family":"Chiocchia","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2833-7997","authenticated-orcid":false,"given":"Johannes","family":"Nossent","sequence":"additional","affiliation":[]},{"given":"Benedicte A.","family":"Lie","sequence":"additional","affiliation":[]},{"given":"\u00d8ystein","family":"F\u00f8rre","sequence":"additional","affiliation":[]},{"given":"Jaakko","family":"Tuomilehto","sequence":"additional","affiliation":[]},{"given":"Kari","family":"Laiho","sequence":"additional","affiliation":[]},{"given":"Linda A.","family":"Bradbury","sequence":"additional","affiliation":[]},{"given":"Dirk","family":"Elewaut","sequence":"additional","affiliation":[]},{"given":"Ruben","family":"Burgos-Vargas","sequence":"additional","affiliation":[]},{"given":"Simon","family":"Stebbings","sequence":"additional","affiliation":[]},{"given":"Louise","family":"Appleton","sequence":"additional","affiliation":[]},{"given":"Claire","family":"Farrah","sequence":"additional","affiliation":[]},{"given":"Jonathan","family":"Lau","sequence":"additional","affiliation":[]},{"given":"Nigil","family":"Haroon","sequence":"additional","affiliation":[]},{"given":"Juan","family":"Mulero","sequence":"additional","affiliation":[]},{"given":"Francisco J.","family":"Blanco","sequence":"additional","affiliation":[]},{"given":"Miguel A.","family":"Gonzalez-Gay","sequence":"additional","affiliation":[]},{"given":"C","family":"Lopez-Larrea","sequence":"additional","affiliation":[]},{"given":"Paul","family":"Bowness","sequence":"additional","affiliation":[]},{"given":"Karl","family":"Gaffney","sequence":"additional","affiliation":[]},{"given":"Hill","family":"Gaston","sequence":"additional","affiliation":[]},{"given":"Dafna D.","family":"Gladman","sequence":"additional","affiliation":[]},{"given":"Proton","family":"Rahman","sequence":"additional","affiliation":[]},{"given":"Walter P.","family":"Maksymowych","sequence":"additional","affiliation":[]},{"given":"J. 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