. Author manuscript; available in PMC: 2016 Jul 3.

Published in final edited form as: Nat Genet. 2015 Jul 13;47(8):898–905. doi: 10.1038/ng.3353

Table 2.

Pairwise haplotypic interactions in HLA-DRB1–HLA-DQA1–HLA-DQB1

		HLA-DRB1	15:01	07:01	04:04	04:01	04:01	03:01	01:01
		HLA-DQA1	01:02	02:01	03:01	03:01	03:01	05:01	01:01
		HLA-DQB1	06:02	02:02	03:02	03:02	03:01	02:01	05:01

		Amino acids	D-R-A	A-Y-R	A-H-R	A-H-K	D-H-K	A-S-K	V-F-R
HLA-DRB1	Amino acids	Additive OR	0.16	0.19	2.77	5.49	1.40	2.83	1.00 (ref)
HLA-DQA1
HLA-DQB1
01:01	V-F-R	1.00 (ref)	0.14	2.32	0.71	2.16	1.95	1.04
01:01			(0.004)	(0.04)	(0.19)	(1.2 × 10⁻⁴)	(7.7 × 10⁻⁴)	(0.77)
05:01
03:01	A-S-K	2.83	0.09	2.24	2.12^a	1.96^a	0.32
05:01			(1.2 × 10⁻⁵)	(0.03)	(1.9 × 10⁻⁴)^a	(1.2 × 10⁻⁵)^a	(9.2 × 10⁻¹¹)
02:01
04:01	D-H-K	1.40	0.26	4.78	0.23	0.48
03:01			(0.03)	(1.1 × 10⁻⁴)	(2.4 × 10⁻⁶)	(1.1 × 10⁻³)
03:01
04:01	A-H-K	5.49	0.36	5.09	0.33
03:01			(0.03)	(4.2 × 10⁻⁵)	(3.5 × 10⁻⁵)
03:02
04:04	A-H-R	2.77	0.62	2.16
03:01			(0.03)	(0.08)
03:02
07:01	A-Y-R	0.19	0.76
02:01			(0.74)
02:02
15:01	D-R-A	0.16
01:02
06:02

The table shows, for each given pair of haplotypes, the fold change in OR (from additive effect only) due to interaction. The amino acids column and row denote the residues at HLA-DQβ1 position 57, HLA-DRβ1 position 13 and HLA-DRβ1 position 71 corresponding to each haplotype. For each haplotype pair, the P value of the interaction term is shown in parentheses. Cells in bold indicate interactions that are significant after Bonferroni correction (P < 0.05/21 = 0.0024). The OR of a given diploid genotype is calculated as additive effect_{haplotype 1} × additive effect_{haplotype 2} × interaction_{haplotype 1, haplotype 2} (Supplementary Table 9).

The known HLA-DR3/HLA-DR4 heterozygote effect.