A GWAS of patients with anti-neutrophil cytoplasmic antibodies (ANCA) found an association between proteinase-3 (PR3) ANCA and a single-nucleotide polymorphism (SNP) (rs62132293) upstream of PRTN3, encoding PR3. The variant (G-allele) was shown to be an eQTL in healthy controls, but the clinical impact remains unknown. Longitudinally followed ANCA patients (n=401) and healthy controls (n=130) were genotyped. Gene expression was quantified by RT-qPCR from leukocyte RNA. Plasma PR3 was quantified by ELISA. Kaplan-Meier estimates and log rank test were used for clinical outcomes. Among patients, variant carriers had elevated leukocyte PRTN3 expression compared to non-carriers (C/G vs. C/C and G/G vs. C/C, p=0.012 and p=0.001, respectively, effect size 0.24). Healthy controls had low PRTN3 regardless of genotype. MPO expression did not differ by genotype. PRTN3 (message) correlated with circulating PR3 (r=0.36, p<0.0005) and variant carriers had higher plasma PR3 compared to noncarriers (p=0.041). Among variant carriers, there was a 1.66-fold increased risk of relapse in patients with PR3-ANCA vs. MPO-ANCA (HR 1.66, 95% CI 1.08, 2.54). The risk allele marked by rs62132293 is clinically significant as it is associated with increased autoantigen and may, in part, explain increased relapse in PR3-ANCA. Our results underscore the role of autoantigen availability in ANCA vasculitis.