Table 4.

Multi-locus model of HIBAG-imputed HLA dosages, single locus and stepwise results

	Dosage Frequency		Best Guess Count
HLA Allele	Cases	Controls	Cases	Controls	OR (95% CIA)	Single Locus P-value	Stepwise P-value	Stepwise OR (95%CIA)
DQB1*0602B	0.25	0.15	301	636	1.90 (1.62 - 2.21)	5.55×10−16	1.93×10−23	2.35 (1.99 – 2.78)
DRB1*0803	0.20	0.13	251	613	1.59 (1.34 - 1.88)	7.37×10−8	7.63×10−16	2.14 (1.78 - 2.58)
DQB1*0202	0.18	0.12	212	502	1.60 (1.35 - 1.90)	7.57×10−8	2.19×10−18	2.50 (2.04 - 3.07)
DQA1*0302	0.19	0.16	286	847	1.41 (1.15 - 1.75)	1.27×10−3	4.92×10−9	1.98 (1.58 - 2.50)
B*0801	0.02	0.004	20	14	5.43 (2.66 - 11.08)	3.42×10−6	5.15×10−6	5.71 (2.70 -12.07)
DQA1*0401	0.04	0.03	54	133	1.73 (1.17 - 2.57)	5.94×10−3	3.11×10−5	2.36 (1.58 - 3.54)
C*0702	0.22	0.17	261	711	1.37 (1.17 - 1.59)	5.45×10−5	2.06×10−3	1.30 (1.10 - 1.54)
DRB1*0406	0.03	0.07	41	354	0.15 (0.09 - 0.26)	2.63×10−11	1.11×10−4	0.32 (0.18 - 0.57)
DPB1*0501	0.79	0.72	930	3092	1.16 (1.05 - 1.28)	2.87×10−3	1.06×10−4	1.23 (1.11 - 1.36)
DRB1*1602	0.03	0.02	38	87	1.78 (1.16 - 2.72)	7.73×10−3	1.53×10−3	2.05 (1.32 - 3.20)
DPB1*1701	0.03	0.04	41	160	0.90 (0.62 - 1.30)	5.66×10−1	1.07×10−3	0.5 (0.33 - 0.76)
C*0102	0.29	0.32	359	1429	0.88 (0.77 - 1.01)	6.51×10−2	5.82×10−3	0.82 (0.71 - 0.94)
DRB1*1202	0.04	0.07	39	266	0.52 (0.37 - 0.74)	2.98×10−4	7.07×10−3	0.61 (0.42 - 0.87)

^ACI = Confidence interval

^BThe allele HLA-DRB1*1501 had the same P-value as HLA-DQB1*0602, but the later was selected by the stepwise modeling procedure. For complete results, please refer to Supplementary Table 5.

Note: Tables are in the order they were identified in the stepwise model. The stepwise results presented in this table are for adjusting for all other variants in the table