Table 2 Single nucleotide polymorphism (SNP) allele frequencies in patients with Wegener’s granulomatosis (WG) and controls

SNP	RefSeq number	Major/minor allele	CEU allele frequencies according to HapMap	MAF in controls	MAF in patients with WG*	p Value
1	rs588997	G/A	0.64/0.36	0.37	0.34	0.198
26	rs1367728	G/A	0.90/0.10	0.12	0.14	0.323
2	rs9469341	A/G	0.88/0.12	0.16	0.08	0.0001
27	rs9277341	T/C	0.78/0.22	0.28	0.13	6.01×10⁻¹⁰
3	rs3117228	C/A	0.68/0.32	0.30	0.08	3.64×10⁻²¹
28	rs2281390	C/A	0.84/0.16	0.18	0.23	0.030
4	rs2064474	C/T	0.79/0.21	0.24	0.05	2.323×10⁻¹⁹
5	rs3130215	G/A	0.56/0.44	0.41 (A)	0.38 (G)	1.946×10⁻¹³
29	rs11751659	A/G	0.85/0.15	0.13	0.15	0.492
6	rs3130233	T/C	0.51/0.49	0.50	0.39	0.0001
7	rs3129269	G/T	0.65/0.35	0.37	0.26	3.35×10⁻⁵
8	rs2294478	G/T	0.59/0.41	0.46	0.49	0.428
9	rs2294477	C/G	0.59/0.41	0.44 (G)	0.43 (C)	4.72×10⁻⁶
10	rs2294473	G/C	0.52/0.48	0.46	0.47	0.522
11	rs9277882	T/G	0.62/0.38	0.44	0.34	0.0004
12	rs7754362	A/C	0.69/0.31	0.43	0.34	0.0019
13	rs3129208	T/C	0.55/0.45	0.37	0.48	0.0001
14	rs9277916	C/G	0.69/0.31	0.32	0.30	0.283
15	rs3116956	G/A	0.65/0.35	0.33	0.45	4.96×10⁻⁶
16	rs734181	G/C	0.78/0.22	0.18	0.15	0.116
17	rs1799910	G/A	0.55/0.45	0.49	0.31	7.71×10⁻¹⁰
18	rs2855423	C/T	0.69/0.31	0.26	0.42	7.63×10⁻¹⁰
19	rs9277934	C/T	0.70/0.30	0.31	0.28	0.276
20	rs421446	T/C	0.74/0.26	0.27	0.14	3.78×10⁻⁹
32	rs213210	T/C	0.94/0.06	0.06	0.01	0.0001
33	rs213209	G/A	0.75/0.25	0.27	0.14	5.45×10⁻⁹
34	rs213208	C/A	0.78/0.22	0.22	0.08	2.14×10⁻¹²
35	rs2854028	G/A	0.77/0.23	0.23	0.22	0.779
21	rs9277936	T/A	0.75/0.25	0.25	0.26	0.611
22	rs213213	G/A	0.68/0.32	0.31	0.49	2.26×10⁻¹⁰
23	rs213194	A/G	0.73/0.27	0.24	0.42	6.82×10⁻¹¹
30	rs9277952	G/A	0.64/0.36	0.11	0.07	0.0059
31	rs460568	G/A	0.81/0.19	0.15	0.18	0.154
24	rs213199	C/T	0.67/0.33	0.36	0.30	0.031
25	rs213207	A/G	0.52/0.48	0.50	0.47	0.288

*MAF from patients with WG and p values are given for the entire cohort (n = 282). For differential data from the original patient cohort (Jagiello et al11), the new ANCA-positive cohort and the ANCA-negative cohort see supplementary table 1.
ANCA, antineutrophil cytoplasmic antibodies; MAF, minor allele frequency.