Background: ANCA-associated vasculitides (AAV) are rare but aggressive autoimmune disorders. The pathogenesis of the disorders is complex and still poorly understood; only a few genetic loci have been associated with AAV. The aim of this project was to identify and characterize novel susceptibility loci for AAV positive for myeloperoxidase (MPO) or proteinase 3 (PR3) ANCA. Methods: Genetic association analyses were performed after Illumina sequencing of 1853 genes and subsequent replication with genotyping of candidate single-nucleotide polymorphisms (SNPs) in a total cohort of 1110 Scandinavian cases with granulomatosis with polyangiitis (GPA) or microscopic polyangiitis (MPA) and 1589 controls. Data were analysed using logistic regression with a P value threshold for significance of < 9.1 x 10-7. A novel AAV-associated SNP was analysed for allele-specific effects on gene expression using luciferase reporter assay. Results: Associations between PR3-ANCA positive (+) AAV and the HLA-DPB1, HLA-DPA1 and SERPINA1 genes and between MPO-ANCA+ AAV and the HLA–DQB1 locus identified in previous genome-wide studies were confirmed in the present study. In addition, a rare SNP located in the BACH2 gene (rs78275221) was identified as significantly associated with MPO-ANCA+ AAV (P = 7.9 x 10-7, Odds ratio = 3.0 in meta-analysis). The rare allele of the novel disease-associated SNP affected downstream gene expression in primary endothelial cells, specifically. Conclusion: This study confirms previous findings of genetic associations specific for PR3-ANCA+ and MPO-ANCA+ AAV, respectively. A novel susceptibility locus for MPO-ANCA+ AAV was identified, where the disease-associated SNP may facilitate the development of autoimmunity through a negative effect on gene expression in specific cell types. Disclosures: None.