Table 2.

Association Analyses Between Amino Acid Variation in the HLA-DRβ1 Chain and PSC^*

		Single-Residue LR		Two-Residue LR†				Three-Residue LR‡
		Basic Model: -		Basic Model: Residue 37		Basic Model: Residue 86		Basic Model: Residues 37+86
Residue	Observed Amino Acids	P-value	Rank	P-value	Rank	P-value	Rank	P-value
9	Glu, Lys,Trp	0.051	27	0.59	22	0.0086	20	0.29
10	Glu,Gln,Tyr	2.4 × 10−11	14	0.54	21	0.0017	17	0.48
11	Asp,Gly,Leu,Pro,Ser,Val	1.2 × 10−18	8	0.23	15	1.7 × 10−8	3	0.43
12	Lys,Thr	2.7 × 10−12	12	0.64	24	0.00046	14	0.74
13	Phe,Gly,His,Arg,Ser,Tyr	9.6 × 10−25	2	0.22	14	2.1 × 10−11	2	0.25
14	Glu,Lys	0.0014	20	0.36	17	0.74	28	0.83
16	His,Tyr	3.2 × 10−5	17	0.88	29	0.00053	15	0.78
25	Gln,Arg	0.0014	21	0.36	18	0.74	29	0.83
26	Phe,Leu,Tyr	2.6 × 10−19	6	0.024	2	3.9 × 10−8	4	0.23
28	Asp,Glu,His	2.8 × 10−5	16	0.13	8	0.0053	19	0.10
30	Cys,Gly,His Leu,Arg,Tyr	0.00012	18	0.12	7	2.0 × 10−5	11	0.20
31	Phe,Ile,Val	0.31	29	0.078	5	0.0046	18	0.12
32	His,Tyr	1.2 × 10−21	4	0.38	19	6.6 × 10−8	6	0.64
33	His,Asn	1.4 × 10−15	11	0.40	20	5.0 × 10−8	5	0.31
37	Phe,Leu,Asn,Ser,Tyr	1.2 × 10−32	1	—		3.1 × 10−16	1	—
38	Ala,Leu,Val	0.029	26	0.17	11	0.0014	16	0.14
40	Phe,Tyr	0.77	30	0.17	12	0.52	27	0.14
47	Phe,Tyr	2.4 × 10−21	5	0.11	6	0.00024	13	0.29
57	Ala,Asp,Ser,Val	2.6 × 10−5	15	0.78	26	0.16	22	0.44
58	Ala,Glu	0.00055	19	0.85	28	0.035	21	0.84
60	His,Ser,Tyr	0.0046	24	0.59	23	0.28	24	0.29
67	Phe,Ile,Leu	0.0018	22	0.80	27	0.45	25	0.22
70	Asp,Gln,Arg	0.063	28	0.16	10	0.49	26	0.32
71	Ala,Glu,Lys,Arg	1.4 × 10−15	10	0.043	3	5.4 × 10−6	8	0.32
73	Ala,Gly	5.5 × 10−12	13	0.14	9	1.7 × 10−5	10	0.34
74	Ala,Glu,Leu,Gln,Arg	1.7 × 10−18	9	0.25	16	9.4 × 10−6	9	0.59
77	Asn,Thr	5.8 × 10−19	7	0.060	4	4.8 × 10−7	7	0.34
78	Val,Tyr	0.023	25	0.77	25	0.25	23	0.20
85	Ala,Val	0.0037	23	0.21	13	7.2 × 10−5	12	0.13
86	Gly,Val	1.8 × 10−22	3	2.0 × 10−5	1	—		—

^*Stepwise logistic regressions were performed assuming an “allele dosage” effect.

^†P-values of likelihood ratio tests of whether residue n improves the logistic regression model when added to a model with one other residue (37 or 86).

^‡P-values of likelihood ratio tests of whether residue n improves the model when added to a model with both residues 37 and residue 86.

LR: likelihood ratio; Rank: residue rank according to P-value, lowest P-value is highlighted in bold.