Table 2 Association of haplotypes defined by eight independent signals with NPC in Hong Kong Chinese.

From: Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci

Haplotype (H)^a	rs9391681	HLA-A_aa-Q62	rs2523589	HLA-B55:02*	rs2517664	rs9265975	rs9461780	rs117495548	Case_H freq	Control_H freq	Total_H freq	OR1	P1	OR2	P2
H1	0	0	0	0	0	0	0	0	0.3530	0.2594	0.3047	1.56	2.90e−27	1.00	1.00e+00
H2	1	0	0	0	0	0	0	0	0.1533	0.0638	0.1071	2.66	1.76e−53	1.77	9.18e−16
H3	0	1	1	0	0	0	0	0	0.0434	0.0785	0.0615	0.53	1.01e−14	0.41	5.61e−26
H4	0	1	1	0	0	1	0	0	0.0109	0.0277	0.0196	0.39	1.44e−10	0.29	4.59e−17
H5	0	1	0	0	0	0	0	0	0.1428	0.1648	0.1542	0.84	1.28e−03	0.64	2.10e−14
H6	0	0	1	0	0	1	0	0	0.0164	0.0300	0.0234	0.54	2.14e−06	0.40	3.78e−12
H7	0	1	0	0	0	0	1	0	0.0091	0.0192	0.0143	0.47	7.62e−06	0.35	3.37e−10
H8	0	0	0	0	0	0	1	0	0.0165	0.0279	0.0224	0.59	5.41e−05	0.44	4.47e−10
H9	0	1	1	1	0	0	0	0	0.0005	0.0060	0.0033	0.09	1.00e−07	0.07	7.87e−10
H10	0	0	1	1	0	0	0	0	0.0016	0.0068	0.0043	0.24	4.72e−05	0.18	2.97e−07
H11	0	1	0	0	1	0	0	0	0.0015	0.0065	0.0040	0.22	4.79e−05	0.17	3.55e−07
H12	0	0	1	0	0	0	0	0	0.1161	0.1171	0.1166	0.99	8.87e−01	0.73	1.12e−06
H13	0	0	0	1	0	0	0	0	0.0009	0.0049	0.0030	0.18	1.68e−04	0.14	3.25e−06
H14	0	1	1	0	1	1	0	0	0.0004	0.0036	0.0020	0.10	7.72e−05	0.07	4.29e−06
H15	0	1	0	0	0	1	0	0	0.0102	0.0160	0.0132	0.63	8.25e−03	0.47	9.51e−06
H16	0	1	1	0	0	0	1	0	0.0031	0.0077	0.0054	0.40	1.46e−03	0.30	1.26e−05
H17	0	0	1	0	0	0	0	1	0.0005	0.0034	0.0020	0.16	5.54e−04	0.12	2.83e−05
H18	0	1	0	1	0	0	0	0	0.0007	0.0037	0.0023	0.19	6.15e−04	0.14	3.06e−05
H19	0	0	0	0	0	0	0	1	0.0036	0.0078	0.0058	0.46	4.76e−03	0.34	5.26e−05
H20	0	0	0	0	1	0	0	1	0.0000	0.0019	0.0010	<0.097	1.03e−03	<0.071	1.21e−04
H21	0	0	1	0	0	0	1	0	0.0067	0.0109	0.0089	0.61	2.31e−02	0.45	1.65e−04
H22	0	0	1	0	1	1	0	0	0.0002	0.0022	0.0012	0.08	1.95e−03	0.06	1.95e−04
H23	0	1	1	0	0	0	0	1	0.0002	0.0022	0.0012	0.08	1.95e−03	0.06	1.95e−04
H24	0	1	1	0	1	0	0	0	0.0033	0.0068	0.0051	0.48	1.18e−02	0.35	2.44e−04

Twenty-four out of 111 haplotypes were significantly associated with NPC passing Bonferroni correction (p < 4.50 × 10⁻⁴). H1 (bolded) indicates individuals predisposed with higher NPC risk when carrying this susceptibility haplotype lacking all seven protective alleles.
OR1 is the raw odds ratio of each haplotype. OR2 (bolded) is the normalized odds ratio relative to H1, which is the most frequent haplotype in Hong Kong Chinese.
^a1 stands for the risk C-allele of rs9391681 in H2 and the other seven protective alleles (HLA-A_aa-Q62, T-allele of rs2517664, A-allele of rs9265975, G-allele of rs2523589, HLA-B*55:02, T-allele of rs9461780, and G-allele of rs117495548) in other haplotypes.

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Table 2 Association of haplotypes defined by eight independent signals with NPC in Hong Kong Chinese.

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