Table 3.

Conditional analyses for independence of SNP signals.

Main SNP	Additional Covariate SNPs	OR [95% CI]	p-value
MN
rs2187668	—	4.48 [3.32–6.11]	2.4 × 10−22
	rs1150754	5.21 [3.32–8.19]	8.1 × 10−13
	rs1129740	4.29 [3.09–5.96]	4.1 × 10−18
	rs9275596	4.67 [3.16–6.90]	9.6 × 10−15
	rs1150754, rs1129740	4,97 [3.10–7.96]	2.7 × 10−11
	rs1150754, rs9275596	5.39 [3.24–8.97]	8.6 × 10−11
	rs1129740, rs9275596	4.11 [2.36–7.17]	6.2 × 10−7
	rs1150754, rs1129740, rs9275596	4.74 [2.49–9.04]	2.2 × 10−6
SLE
rs2187668	—	2.36 [1.63–3.42]	5.9 × 10−6
	rs1150754	2.12 [1.22–3.70]	8.0 × 10−3
	rs7763262	1.96 [1.30–2.95]	1.3 × 10−3
	rs9275596	1.94 [1.26–3.00]	2.7 × 10−3
	rs1150754, rs7763262	1.86 [1.04–3.33]	3.6 × 10−2
	rs1150754, rs9275596	1.72 [0.94–1.36]	8.0 × 10−2
	rs7763262, rs9275596	1.93 [1.25–2.97]	3.0 × 10−3
	rs1150754, rs7763262, rs9275596	1.81 [0.97–3.37]	6.1 × 10−2
GPA
rs660895	—	1.81 [1.32–2.47]	2.0 × 10−4
	rs9277554	1.73 [1.26–2.38]	7.3 × 10–4
rs9277554	—	0.14 [0.08–0.25]	1.7 × 10−11
	rs660895	0.14 [0.08–0.25]	2.6 × 10−11
T1DM
rs1150754	—	2.53 [1.78–3.60]	2.5 × 10−7
	rs660895	2.75 [1.91–3.98]	7.2 × 10−8
	rs1129740	2.12 [1.47–3.05]	5.5 × 10−5
	rs660895, rs1129740	2.62 [1.78–3.85]	1.0 × 10−6
rs660895	—	3.00 [2.17–4.18]	4.6 × 10−11
	rs1150754	3.19 [2.28–4.46]	1.5 × 10−11
	rs1129740	2.47 [1.72–3.56]	1.2 × 10−6
	rs1150754, rs1129740	2.93 [2.00–4.30]	3.6 × 10−8

All SNPs with independent associations with the examined etiology are displayed. Associations were defined as independent if they stayed statistically significant in all performed conditional analyses and ORs did not vary by >20%. Although rs2187668 did not show independence for significant association with SLE throughout, it is shown here because it had the lowest p-value of all SNPs associated with SLE and an OR variation of <20%. For complete data see Supplementary Table 7. MN: Membranous nephropathy, IgA: IgA nephropathy, SLE: Systemic lupus erythematosus, GPA: Granulomatosis with polyangiitis, T1DM: Type 1 diabetes mellitus, OR: Odds ratio, CI: Confidence interval.