Table 2. The ten independent epistatic pairs of SNPs within MHC and their interaction P values conditioning on the additive background in RACI-UK and without conditioning on the additive background in each of the three study cohorts^*.

SNP1	Position1	SNP2	Position2	Conditional_P	Unconditional_P_UK	Unconditional_P_US	Unconditional_P_SE
rs805286	31 711 530	rs532098	32 610 275	2.5e-07	1.3e-16	6.9e-04	4.6e-04
rs9266629	31 379 045	rs3830076	32 128 467	1.0e-04	2.2e-14	4.4e-04	1.5e-04
rs9267833	32 210 123	rs2858312	32 699 453	2.5e-03	2.3e-14	2.2e-18	9.9e-12
rs3177928	32 444 658	rs9368737	32 690 652	5.6e-04	7.7e-16	2.9e-02	1.0e-02
rs3997849	32 714 625	rs3892710	32 715 085	3.2e-05	1.9e-38	5.0e-18	3.2e-15
rs9366778	31 301 396	rs2239707	31 557 542	7.1e-04	1.6e-14	8.7e-02	2.6e-03
rs2517448	31 094 890	rs2256594	32 219 095	3.2e-04	3.3e-17	1.3e-05	2.8e-02
rs4947342	32 685 293	rs2857126	32 809 363	1.0e-03	6.5e-13	1.0e-03	2.2e-02
rs241433	32 831 018	rs2239701	32 837 272	7.9e-04	9.5e-24	5.1e-07	6.2e-03
rs2736426	31 777 507	rs11244	32 812 946	6.3e-04	2.0e-16	4.6e-04	2.3e-12

^*SNP₁₍₂₎: the first (second) epistatic SNP; Position₁₍₂₎: the genomic postion of the SNP₁₍₂₎; Conditional_P: the interaction P value in the final model fitting covariates, the additive effects of the 20 independent GWAS SNPs and the 10 epistatic pairs of SNPs and their interactions; Unconditional_P_UK (US or SE): the interaction P value corrected for covariates but not the additive background in RACI-UK (US or SE); P values greater than 0.05 underlined.