Table 1. Intra- and inter-haplotypic comparisons: SNVs and indels.

Variant Type	Intra-CEH				Inter-haplotype
	A2-B46-DR9	A33-B58-DR3	A2-B46-DR9 vs A33-B58-DR3	A2-B46-DR9 vs PGF	A33-B58-DR3 vs PGF	A2-B46-DR9 vs COX	A33-B58-DR3 vs COX	PGF vs COX
SNVs
Coding	2	1	161	126	204	160	206	190
Missense	1	1	84	68	111	91	113	99
Nonsense	0	0	1	2	1	0	1	2
Synonymous	1	0	76	56	92	69	92	89
ncRNA exonic	0	0	138	106	119	148	152	115
UTR 5’	1	1	24	28	34	24	32	37
UTR 3’	0	11	75	54	87	64	79	78
Intronic	32	38	1745	1320	1704	1577	1859	1529
Promoter region	6	5	217	228	242	267	222	195
Intergenic	197	234	5141	4250	6795	4779	6549	7911
Total	238	290	7501	6112	9185	7019	9099	10055
SNVs/100kb	8.58	6.84	270	220	211	253	217	237
Indels
Coding	0	0	3	2	2	5	4	3
Frameshift	0	0	3	2	2	3	3	1
Non-frameshift	0	0	0	0	0	2	1	2
ncRNA exonic	1	0	17	9	18	18	24	19
UTR	1	1	12	6	18	9	16	15
Intronic	9	12	208	135	180	298	363	381
Promoter region	3	2	26	19	19	37	44	36
Intergenic	37	37	418	298	516	688	993	1298
Total	51	52	684	469	753	1055	1444	1752
Indels/100kb	1.80	1.22	24.6	16.9	17.3	37.9	34.4	41.2

BED files of the PGF and COX ⁹,¹⁷,¹⁸ were downloaded from http://www.ucl.ac.uk/cancer/medical-genomics/mhc/#HaplotypeData and the coordinates of these BED files were aligned to the Human Reference Sequence Assembly 37.2 (NCBI build 37.2).