Table 7.
SNP counts and crossover (XO) loci between linked HLA-C and HLA-B alleles using different combinations of haplotype pairs.
| Alignments between haplotypes | Number of SNPs per section | XO | SNP or | closest | XO nt distance | XO in or | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Lab ID numbers precede haplotypes | 0–7 k | 7–10 kb HLA-C | 10–20 k | 20–40 k | 40–60 k | 60–80 k | 80–93 k HLA-B | 0–93 k | Location bp | Indel at XO | Repeat | To end of HLA-B exon 8 | Between (/) HLA-C and -B | |
| Haplotype 1 | Haplotype 2 | |||||||||||||
| (A) Different HLA-C/HLA-B haplotypes | ||||||||||||||
| 66_C*02/B*27:05 | 49_C*08:02/B*14:02 | 33 | 32 | 85 | 114 | 455 | 805 + MI | 269 | 1,811 | none | 0 | nd | 0 | SRR |
| 55_C*06:02/B*13:02 | 95_C*07/B*57 | 15 | 88 | 85 | 112 | 247 + MI | 768 | 185 | 1,500 | none | 0 | nd | 0 | SRR |
| (B) Same HLA-C/ HLA-B haplotypes | ||||||||||||||
| 28_C*03:03/B*15 | 17_C*03:03/B*15 | 0 | 0 | 0 | 1 | 0 | 2 | 2 | 5 | 0 | 0 | nd | 0 | SPR |
| 54_C*04/B*35 | 23_C*04/B*35 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 2 | 0 | 0 | nd | 0 | SPR |
| 55_C*06:02/B*13:02 | 91_C*06:02/B*13 | 0 | 0 | 1 | 0 | 0 | 0 | 0 + indels | 1 | 0 | 0 | nd | 0 | SPR |
| 6_C*07/B*07:02 | 4_C*07/B*07:02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | nd | 0 | SPR |
| 11_C*07/B*08 | 12_C*07/B*08 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | nd | 0 | SPR |
| 65_C*08:02/B*14:01 | 49_C*08:02/B*14:02 | 0 | 0 | 0 | 0 | 0 | 0 | 77 | 77 | 0 | 0 | nd | 0 | SPR |
| (C) Same HLA-C allele–different HLA-B allele | ||||||||||||||
| 6_C*07/B*07:02 | 30_C*07/B*18 | 12 | 9 + XO | 68 | 89 | SRR | SRR | SRR | SRR | HLA-C*7 | 0 | nd | nd | HLA-C |
| 30_C*07/B*18 | 6_C*07/B*07:02 | 12 | 9 + XO | 68 | 89 | SRR | SRR | SRR | SRR | HLA-C*7 | 0 | nd | nd | HLA-C |
| 6_C*07/B*07:02 | 8_C*07:18/B*58 | 19 | 9 + XO | 122 | 163 | SRR | SRR | SRR | SRR | HLA-C*7 | 0 | nd | nd | HLA-C |
| 8_C*07:18/B*58 | 6_C*07/B*07:02 | 19 | 9 + XO | 122 | 163 | SRR | SRR | SRR | SRR | HLA-C*7 | 0 | nd | nd | HLA-C |
| 94_C*12:03/B*51 | 56_C*12:02/B*52 | 41 | XO + 24 | 76 | 195 | SRR + MI | SRR | 41 | SRR | HLA-C*12 | 0 | nd | nd | HLA-C |
| 94_C*12:03/B*51 | 53__C*12:02/B*52 | 41 | 2 + XO | 70 | 217 | SRR | SRR | 41 | SRR | HLA-C*12 | 0 | nd | nd | HLA-C |
| 11_C*07/B*08 | 8_C*07:18/B*58 | 169 | 4 | 2+XO+2 | 163 | 32 | 277 + MI | 387 | 1036 | 19961 | A/G | L1PA13 | 72,286 | HLA-C/HLA-B |
| 11_C*07/B*08 | 30_C*07/B*18 | 159 | 0 | 0+XO+2 | 91 | 327 + MI | 348 + MI | 341 | 1268 | 19961 | A/G | L1PA13 | 72,286 | HLA-C/HLA-B |
| 11_C*07/B*08 | 42_C*07/B*49 | 159 | 0 | 0+XO+2 | 89 | 329 + MI | 348 + MI | 376 | 1303 | 19961 | A/G | L1PA13 | 72,286 | HLA-C/HLA-B |
| 11_C*07/B*08 | 95_C*07/B*57 | 1 | 0 | 0+XO+1 | 91 | 327 + MI | 348 + MI | 373 | 1141 | 19961 | A/G | L1PA13 | 72,286 | HLA-C/HLA-B |
| 92_C*01/B*51 | 39_C*01/B*27:05 | 0 | 0 | 1 | XO+30 | 367 | 578 + 5k MI | 240 | 1216 | 33326 | C/T | MIR/L1MB8 | 55,903 | HLA-C/HLA-B |
| 39_C*01/B*27:05 | 92_C*01/B*51 | 0 | 0 | 1 | XO+SRR | SRR | SRR | SRR | SRR | 32511 | C/T | MIR/L1MB8 | 60,958 | HLA-C/HLA-B |
| 39_C*01/B*27:05 | 70_C*01/B*46 | 2 | 1 | 2 | XO+SRR | SRR | SRR | SRR | SRR | 35360 | T/A | AluY/MLT1D | 58,109 | HLA-C/HLA-B |
| 39_C*01/B*27:05 | 89_C*01/B*54 | 26 | 0 | 2 | XO+SRR | SRR | SRR | SRR | SRR | 35360 | T/A | AluY/MLT1D | 58,109 | HLA-C/HLA-B |
| 39_C*01/B*27:05 | 59_C*01/B*56 | 2 | 0 | 2 | XO+SRR | SRR | SRR | SRR | SRR | 35360 | T/A | AluY/MLT1D | 58,109 | HLA-C/HLA-B |
| 39_C*01/B*27:05 | 73_C*01/B*15 | 1 | 1 | 2 | XO+SRR | SRR | SRR | SRR | SRR | 35360 | T/A | AluY/MLT1D | 58,109 | HLA-C/HLA-B |
| 11_C*07/B*08 | 4_C*07/B*07:02 | 158 | 7 | 67 | 0 | 0 + XO +217 | SRR + MI | SRR | SRR | 47841 | C/T | MIR | 44,406 | HLA-C/HLA-B |
| 11_C*07/B*08 | 6_C*07/B*07:02 | 158 | 7 | 67 | 0 | 0 + XO + 217 | SRR + MI | SRR | SRR | 47841 | C/T | MIR | 44,406 | HLA-C/HLA-B |
| 55_C*06:02/B*13:02 | 31_C*06:02/B*40 | 0 | 0 | 0 | 0 | 0 | XO+529 | 210 | 739 | 60351 | G/T | HERVI | 21,449 | HLA-C/HLA-B |
| 5_C*05/B*18 | 9_C*05/B*44:02 | 0 | 0 | 0 | 1 | 0 | 0 | XO+87 | 88 | 89798 | T/C | MLT1N2 | 3,827 | 3′HLA-B |
| 95_C*07/B*57 | 30_C*07/B*18 | 160 | 0 | 1 | 0 | 1 | 2 | XO+147 | 319 | 87226 | A/C | MLT1N2/MER5 | 2,767 | 3′HLA-B |
| 28_C*03:03/B*15 | 13_C*03:04/B*40:01 | 5 | 1 | 2 | 2 | 5 | 3 | XO+184 | 204 | 88616 | indel 36bp | MLT1N2/MER5 | 2,478 | 3′HLA-B |
| 28_C*03:03/B*15 | 34_C*03:04/B*40:01 | 5 | 2 | 2 | 2 | 5 | MI + 3 | XO+185 | 205 | 88616 | indel 36bp | MLT1N2/MER5 | 2,478 | 3′HLA-B |
| 54_C*04/B*35 | 48_C*04/B*15:26N | 0 | 0 | MI + 0 | 1 | 0 | 17 | XO+152 | 170 | 88190 | C/T | MLT1N2/MER5 | 2,440 | 3′HLA-B |
| 54_C*04/B*35 | 61_C*04/B*53 | 0 | 0 | 1 | 1 | 0 | 1 | XO+7 | 10 | 88194 | T/C | MLT1N2/MER5 | 2,436 | 3′HLA-B |
| 50_C*14:03/B*44:03 | 88_C*14:02/B*51 | 0 | 0 | 2 | 6 | 1 | 2 | 5+XO+158 | 174 | 99804 | C/A | MLT1N2/MER5 | 2,273 | 3′HLA-B |
| 30_C*07/B*18 | 95_C*07/B*57 | 160 | 0 | 1 | 0 | 1 | 2 | XO+147 | 319 | 93101 | A/C | MLT1N2/MER5 | 2,268 | 3′HLA-B |
| 94_C*12:03/B*51 | 22__C*12:03/B*38 | 0 | 0 | 0 | 0 | 0 | 0 | XO+182 | 182 | 80294 | G/A | MLT1N2/MER5 | 2,226 | 3′HLA-B |
| 66_C*02:02/B*27:05 | 38_C*02/B*40:02 | 0 | 0 | 1 | 0 | 0 | 0 | XO+33 | 34 | 88896 | indel 5bp | MLT1N2/MER5 | 2,165 | 3′HLA-B |
| 55_C*06:02/B*13:02 | 77_C*06:02/B*47 | 0 | 0 | 0 | 0 | 1 | 0 | XO+119 | 120 | 80217 | G/C | L2 | 1,583 | 3′HLA-B |
| 55_C*06:02/B*13:02 | 36_C*06:02/B*57 | 0 | 0 | 0 | 0 | 0 | 2 | XO+187 | 189 | 81180 | G/A | L2 | 620 | 3′HLA-B |
| 55_C*06:02/B*13:02 | 2_C*06:02/B*57 | 0 | 0 | 0 | 0 | 0 | 3 | XO+187 | 190 | 81180 | G/A | L2/HLA-B | 620 | 3′HLA-B |
| 55_C*06:02/B*13:02 | 43_C*06:02/B*37 | 0 | 0 | 0 | 0 | 0 | 3 | XO+190 | 193 | 81180 | G/A | L2/HLA-B | 620 | 3′HLA-B |
| 92_C*01/B*51 | 73_C*01/B*15 | 0 | 0 | 1 | 0 | 0 | 0 | XO+125 | 126 | 88668 | G/A | L2/HLA-B | 560 | 3′HLA-B |
| 92_C*01/B*51 | 59_C*01/B*56 | 0 | 0 | 1 | 0 | 0 | 1 | XO+241 | 242 | 88668 | G/A | L2/HLA-B | 560 | 3′HLA-B |
| 92_C*01/B*51 | 70_C*01/B*46 | 0 | 0 | 1 | 1 | 0 | 0 | XO+127 | 129 | 88668 | G/A | L2/HLA-B | 560 | 3′HLA-B |
| 92_C*01/B*51 | 89_C*01/B*54 | 18 | 0 | 0 | 0 | 0 | 0 | XO+168 | 207 | 88787 | indel 22bp | L2/HLA-B | 441 | 3′HLA-B |
| 83_C*16/B*44:03 | 80_C*16/B*45 | 0 | 0 | 0 | 2 | 0 | 2 | XO+133 | 137 | 91097 | indel | L2/HLA-B | 503 | 3′HLA-B |
| 29_C*17/B*41 | 14_C*17/B*42 | 0 | 0 | 0 | 1 | 0 | 2 | XO+205 | 208 | 86647 | G/A | HLA-B exon 3 | −2,542 | HLA-B (ex 3) |
| (D) Different HLA-C allele/same HLA-B allele | ||||||||||||||
| 92_C*01/B*51 | 94_C*12/B*51 | 176 | 132 | 79 + MI | 791 + MI | 190 + XO | 1368 | 89594 | G/A | HLA-B exon 8 | −186 | HLA-B exon 8 | ||
| 5_C*05/B*18 | 30_C*07/B*18 | SRR | SRR | SSR + MI (5.2kb) | SRR | SRR +XO | SRR + MI | 93767 | G/A | HLA-B exon 8 | −142 | HLA-B exon 8 | ||
| 9_C*05/B*4402 | 83_C*16/B*4403 | SRR | SRR | SRR | SRR + MI | SRR +XO | SRR + MI | 92080 | C/A | L2/HLA-B | 139 | 3′HLA-B | ||
| 92_C*01/B*51 | 46_C*15/B*51 | 141 | 295 | 222 | 149 | 140 + XO | 947 | 89065 | A/T | L2/HLA-B | 163 | 3′HLA-B | ||
| 9_C*05/B*4402 | 50_C*14/B*4403 | SRR | SRR | SRR + MI | SRR + MI | SRR +XO | SRR + MI | 91971 | T/C | L2/HLA-B | 248 | 3′HLA-B | ||
| 73_C*01/B*15 | 28_C*03/B*15 | SRR | SRR | SRR | SRR + MI | SRR + XO | SRR + MI | 87246 | A/G | L2/HLA-B | 640 | 3′HLA-B | ||
| 73_C*01/B*15 | 48_C*04/B*1525N | SRR | SRR | SRR | SRR + MI | SRR + XO | SRR + MI | 87246 | A/G | L2/HLA-B | 640 | 3′HLA-B | ||
| 2_C*06/B*57 | 95_C*07/B*57 | SRR | SRR | SRR + MI | SRR | SRR +XO | SRR + MI | 83390 | A/G | L2/HLA-B | 650 | 3′HLA-B | ||
| 54_C*04/B*35 | 20_C*12/B*35 | SRR + MI | SRR + MI | SRR + MI | SRR | SRR +XO | SRR + MI | 89662 | C/A | L2 | 968 | 3′HLA-B | ||
| 39_C*01/B*27:05 | 66_C*02/B*27:05 | 175 | 79+XO+0 | 0 | 0 | 0 | 254 | 35005 | T/A | L1MB8/MLT1D | 58523 | HLA-C/HLA-B | ||
| 38_C*02/B*40:02 | 34_C*03/B*40:02 | SRR | SRR | SRR | SRR + MI | SRR | SRR | nd | 0 | nd | nd | SRR | ||
| 38_C*02/B*40:02 | 77_C*06/B*40:01 | SRR | SRR | SRR + MI | SRR | SRR | SRR | nd | 0 | nd | nd | SRR | ||
SRR is SNP-rich region that is estimated to be >100 SNP without manual counts, SPR is SNP-poor region (<10 SNP), and MI is major indel (>1 kb usually <6 kb). XO in columns is crossover and XO + number presents the number of SNPs before or after the crossover in each of the 20-kb genomic sections. nd, not determined.