Objective: To identify and characterize genetic loci associated with the risk of developing ANCA-associated vasculitides (AAV).

Methods: Genetic association analyses were performed after Illumina sequencing of 1853 genes and subsequent replication with genotyping of selected single nucleotide polymorphisms in a total cohort of 1110 Scandinavian cases with granulomatosis with polyangiitis or microscopic polyangiitis, and 1589 controls. A novel AAV-associated single nucleotide polymorphism was analysed for allele-specific effects on gene expression using luciferase reporter assay.

Results: PR3-ANCA⁺ AAV was significantly associated with two independent loci in the HLA-DPB1/HLA-DPA1 region [rs1042335, P = 6.3 × 10⁻⁶¹, odds ratio (OR) 0.10; rs9277341, P = 1.5 × 10⁻⁴⁴, OR 0.22] and with rs28929474 in the SERPINA1 gene (P = 2.7 × 10⁻¹⁰, OR 2.9). MPO-ANCA⁺ AAV was significantly associated with the HLA-DQB1/HLA-DQA2 locus (rs9274619, P = 5.4 × 10⁻²⁵, OR 3.7) and with a rare variant in the BACH2 gene (rs78275221, P = 7.9 × 10⁻⁷, OR 3.0), the latter a novel susceptibility locus for MPO-ANCA⁺ granulomatosis with polyangiitis/microscopic polyangiitis. The rs78275221-A risk allele reduced luciferase gene expression in endothelial cells, specifically, as compared with the non-risk allele.

Conclusion: We identified a novel susceptibility locus for MPO-ANCA⁺ AAV and propose that the associated variant is of mechanistic importance, exerting a regulatory function on gene expression in specific cell types.