Table 2.

Logistic regression and conditional analysis of HLA classical alleles in EA SSc

		Frequency (%)†	Unconditioned		Conditioned
	HLA allele	(SSc/Ctrls)	OR (95% CI)	P value	OR (95% CI)	P value
All SSc vs. controls	HLA-DQB1*02:02	10.2/18.0	0.5 (0.4-0.6)	3.55 × 10−9	0.5 (0.4-0.6)	3.55 × 10−9‡
SSc = 723; Control = 5,437	HLA-DRB1*07:01	15.1/23.7	0.5 (0.4-0.7)	6.06 × 10−9
	HLA-DQA1*02:01	15.8/24.3	0.6 (0.4-0.7)	1.04 × 10−8
	HLA-DPB1*13:01	8.3/3.3	2.6 (1.9-3.5)	1.75 × 10−8	2.6 (1.9-3.6)	1.04 × 10−8
	HLA-DRB1*11:04	10.5/4.7	2.2 (1.7-2.9)	9.25 × 10−8	2.0 (1.5-2.7)	1.04 × 10−8
	HLA-B*44:03	5.1/9.7	0.5 (0.3-0.7)	4.72 × 10−6
	HLA-DRB1*01:01	23.7/17.3	1.5 (1.2-1.8)	4.39 × 10−5
AFA+ SSc vs. controls	Not tested
SSc = 0; control = 5,437
ATA+ SSc vs. controls	HLA-DPB1*13:01	32.2/3.3	13.7 (8.9-21.0)	1.47 × 10−24	13.7 (8.9-21.0)	1.47 × 10−24‡
SSc = 115; control = 5,437	HLA-DRB1*11:04	25.2/4.7	6.3 (3.9-10.0)	8.62 × 10−12	6.5 (4.0-10.6)	1.59 × 10−11
	HLA-DPA1*02:01	48.7/26.3	2.9 (2.0-4.2)	8.70 × 10−8
	HLA-DPA1*01:03	54.8/32.6	2.7 (1.8-3.9)	4.65 × 10−7
ARA+ SSc vs. controls	None significant
SSc = 123; control = 5,437
ACA+ SSc vs. controls	HLA-DRB1*07:01	3.4/23.7	0.1 (0.05-0.2)	4.79 × 10−20	0.1 (0.05-0.2)	4.79 × 10−20‡
SSc = 238; control = 5,437	HLA-DQA1*02:01	4.6/14.5	0.1 (0.1-0.2)	4.85 × 10−18
	HLA-DQB1*02:02	2.9/18.0	0.1 (0.1-0.3)	2.44 × 10−14
	HLA-DQB1*05:01	42.4/22.3	2.3 (1.8-3.0)	4.21 × 10−9	2.0 (1.5-2.6)	2.93 × 10−6
	HLA-DQA1*01:01	47.5/26.7	2.2 (1.7-2.9)	7.08 × 10−9
	HLA-DRB1*01:01	34.5/17.3	2.2 (1.7-3.0)	1.32 × 10−7
	HLA-DQA1*04:01	14.3/5.4	2.7 (1.8-4.0)	4.18 × 10−6	2.7 (1.8-4.0)	6.67 × 10−6
	HLA-DQB1*03:03	2.1/8.9	0.2 (0.1-0.5)	6.29 × 10−6
	HLA-DRB1*08:01	11.8/4.6	2.6 (1.7-3.9)	4.97 × 10−5

Independent associations by conditional regression analyses are shown in bold.

^†Frequency of individuals with 1 or 2 alleles.

^‡Unconditioned; Common EA haplotypes: HLA-DRB1*11:04/DQA1*05:01/DQB1*03:01 and HLA-DRB1*07:01/DQA1*02:01/DQB1*02:02.