Table 2.

Top genetic associations in the HLA region in PR3-AAV and MPO-AAV, respectively

Trait	Conditioned variant(s)*	Allele†	SNP ID (minor allele)	MAF cases	MAF controls	P value	OR	95% CI
PR3-AAV	0	HLA-DPB1*04:01	–	0.74	0.42	7.1×10−38	3.3	2.8 to 4.0
		chr6:33 052 958	rs1042335 (T)	0.038	0.27	6.3×10−35	0.089	0.059 to 0.13
		chr6:33 052 950	rs1042331 (C)	0.035	0.27	7.3×10−35	0.083	0.055 to 0.12
		HLA-DPB1*03:01	–	0.02	0.076	4.1×10−8	0.23	0.13 to 0.37
	HLA-DPB1*04:01	chr6:33 052 950	rs1042331 (C)	0.035	0.27	1.8×10−21	0.13	0.082 to 0.19
		chr6:33 052 958	rs1042335 (T)	0.038	0.27	3.7×10−21	0.14	0.090 to 0.20
		HLA-DPB1*04:02	–	0.12	0.11	1.9×10−16	3.7	2.7 to 5.1
	HLA-DPB1*04:01, HLA-DPB1*04:02	chr6:33 052 950	rs1042331 (C)	0.035	0.27	3.0×10−15	0.17	0.10 to 0.26
		chr6:33 052 958	rs1042335 (T)	0.038	0.27	7.8×10−15	0.18	0.11 to 0.27
		HLA-DPB1*02:01	–	0.056	0.12	3.6×10−8	3.5	2.2 to 5.4
	HLA-DPB1*04:01, chr6:33 052 950	chr6:33 048 640	rs1042140 (G)	0.057	0.21	8.8×10−10	0.26	0.17 to 0.39
	HLA-DPB1*04:01, chr6:33052950, chr6:33 048 640	–
MPO-AAV	0	HLA-DRB1*04:04	–	0.22	0.06	4.5×10−16	4.5	3.1 to 6.4
		chr6:32 609 479	rs35874654 (A)	0.44	0.20	4.2×10−13	3.8	2.7 to 5.5
		chr6:32 635 954	rs9274619 (A)	0.35	0.14	1.9×10−12	3.6	2.5 to 5.1
		HLA-DQB1*03:02	–	0.36	0.14	4.8×10−11	3.4	2.3 to 4.8
	HLA-DRB1*04:04	–

*Variant(s) conditioned for in the association analysis.

†Top two HLA classical alleles and SNPs, respectively, associated with PR3-AAV and MPO-AAV (unadjusted p <5.0 × 10^–8) after conditioning on the indicated variant(s). SNPs are indicated by genomic position (hg19).

ANCA, antineutrophil cytoplasmic antibody; HLA, human leucocyte antigen; MAF, minor allele frequency; MPO, myeloperoxidase; MPO-AAV, MPO-ANCA positive AAV; PR3, proteinase 3; PR3-AAV, PR3-ANCA positive ANCA-associated vasculitis; SNP, single nucleotide polymorphism.