Table 2.

RA associations with variation at amino acids before and after conditioning on the most highly associated amino acid positions 11, 13 and 33.

Amino acid position	RA associated p value	p value after conditioning on position 11	p value after conditioning on position 13	p value after conditioning on position 33
33	2.14E-28	0.0043	N/A	--
13	1.16E-27	0.015	--	0.0072
11	3.39E-26	--	0.49	0.0093
12	7.74E-17	N/A	N/A	0.0027
10	7.88E-16	0.004	0.27	0.0013
47	8.30E-14	0.35	0.39	0.0094
67	3.11E-13	0.27	0.27	0.048
70	5.78E-10	0.007	0.28	0.0053
37	2.30E-05	0.43	0.47	0.69
71	2.58E-05	0.7	0.84	0.19
58	3.84E-05	0.32	0.38	0.062
32	0.0003	0.96	0.072	0.54
40	0.04	0.004	0.27	0.004
26	0.08	0.48	0.72	0.012
31	0.08	0.004	0.27	0.001
73	0.1	0.16	0.13	0.43
38	0.12	0.009	0.28	0.013
74	0.15	0.53	0.27	0.68
16	0.18	0.68	N/A	0.84
86	0.19	0.32	0.88	0.67
57	0.33	0.73	0.67	0.38
60	0.56	0.58	0.65	0.30
30	0.57	0.69	0.68	0.32
28	0.72	0.46	0.056	0.00044
9	0.73	N/A	0.49	0.17
85	0.86	0.32	0.91	0.15
14	0.95	N/A	N/A	0.49
25	0.95	N/A	N/A	0.49
78	0.96	N/A	0.95	0.22

N/A means that the effect at the position in question was completely collinear with the conditioned variable, i.e., there were no polymorphic residues to test with case/ control status after conditioning on a position.