TABLE 5.
Haplotypes, haplotype frequency, D′ values and CO% for the pairwise LD analysis of HERVK9 insertion or deletion and HLA-A alleles in Japanese, African Americans, Australian Caucasians, and the combination of all three populations
| All three populations
|
African American
|
Australian Caucasian
|
Japanese
|
|||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Haplotype | HLA-A | HERVK9.HG | n | Frequency | D′ | CO% | n | Frequency | D′ | CO% | n | Frequency | D′ | CO% | n | Frequency | D′ | CO% |
| 1 | 1 | D | 71 | 0.0975 | 1 | 0 | 8 | 0.0435 | 1 | 0 | 62 | 0.1792 | 1 | 0 | 1 | 0.0051 | 1 | 0 |
| 2 | 2 | D | 167 | 0.2294 | 0.972 | 33 | 0.1793 | 1 | 0 | 85 | 0.2457 | 0.968 | 49 | 0.2475 | 0.966 | |||
| 3 | 2 | I | 2 | 0.0027 | 0.972 | 1.18 | 1 | 0.0029 | 0.968 | 1.16 | 1 | 0.0051 | 0.966 | 2 | ||||
| 4 | 3 | D | 2 | 0.0027 | 0.935 | 3.77 | 1 | 0.0054 | 0.845 | 10 | 1 | 0.0029 | 0.963 | 2.38 | ||||
| 5 | 3 | I | 51 | 0.0701 | 0.935 | 9 | 0.0489 | 0.845 | 42 | 0.1214 | 0.963 | |||||||
| 6 | 11 | D | 16 | 0.0220 | 0.497 | 29.09 | 2 | 0.0109 | 1 | 14 | 0.0707 | 0.283 | ||||||
| 7 | 11 | I | 39 | 0.0536 | 0.497 | 29 | 0.0838 | 1 | 0 | 10 | 0.0505 | 0.283 | 41.7 | |||||
| 8 | 20 | I | 1 | 0.0014 | 1 | 1 | 0.0051 | 1 | ||||||||||
| 9 | 23 | I | 16 | 0.0220 | 1 | 0 | 15 | 0.0815 | 1 | 0 | 1 | 0.0029 | 1 | |||||
| 10 | 24 | D | 2 | 0.0027 | 0.972 | 1.67 | 2 | 0.0101 | 0.942 | |||||||||
| 11 | 24 | I | 120 | 0.1648 | 0.972 | 9 | 0.0489 | 1 | 0 | 36 | 0.1040 | 1 | 0 | 75 | 0.3788 | 0.942 | 2.6 | |
| 12 | 25 | D | 2 | 0.0027 | 1 | 2 | 0.0058 | 1 | ||||||||||
| 13 | 26 | D | 27 | 0.0371 | 0.836 | 1 | 0.0054 | 0.227 | 9 | 0.0260 | 1 | 0 | 17 | 0.0859 | 0.904 | |||
| 14 | 26 | I | 2 | 0.0027 | 0.836 | 6.9 | 1 | 0.0054 | 0.227 | 1 | 0.0051 | 0.904 | 5.56 | |||||
| 15 | 29 | D | 30 | 0.0412 | 0.852 | 11 | 0.0598 | 1 | 0 | 19 | 0.0549 | 0.741 | ||||||
| 16 | 29 | I | 2 | 0.0027 | 0.852 | 6.25 | 2 | 0.0058 | 0.741 | 9.52 | ||||||||
| 17 | 30 | D | 37 | 0.0508 | 0.878 | 26 | 0.1413 | 0.798 | 11 | 0.0318 | 1 | 0 | ||||||
| 18 | 30 | I | 2 | 0.0027 | 0.878 | 5.13 | 2 | 0.0109 | 0.798 | |||||||||
| 19 | 31 | I | 38 | 0.0522 | 0.878 | 5 | 0.0272 | 1 | 12 | 0.0347 | 0.774 | 21 | 0.1061 | 1 | 0 | |||
| 20 | 31 | D | 2 | 0.0027 | 0.914 | 2 | 0.0058 | 0.774 | 14.28 | |||||||||
| 21 | 32 | D | 17 | 0.0234 | 1 | 0 | 6 | 0.0326 | 1 | 11 | 0.0318 | 1 | 0 | |||||
| 22 | 33 | I | 23 | 0.0316 | 1 | 0 | 14 | 0.0761 | 1 | 0 | 3 | 0.0087 | 1 | 0 | 6 | 0.0303 | 1 | 0 |
| 23 | 34 | D | 5 | 0.0069 | 0.039 | 5 | 0.0272 | 0.141 | ||||||||||
| 24 | 34 | I | 4 | 0.0055 | 0.039 | 44.44 | 4 | 0.0217 | 0.141 | 44.44 | ||||||||
| 25 | 36 | I | 3 | 0.0041 | 1 | 3 | 0.0163 | 1 | ||||||||||
| 26 | 43 | D | 1 | 0.0014 | 1 | 1 | 0.0054 | 1 | ||||||||||
| 27 | 66 | D | 3 | 0.0041 | 0.407 | 3 | 0.0163 | 0.292 | ||||||||||
| 28 | 66 | I | 1 | 0.0014 | 0.407 | 25 | 1 | 0.0054 | 0.292 | 25 | ||||||||
| 29 | 68 | D | 27 | 0.0371 | 0.836 | 10 | 0.0543 | 0.528 | 17 | 0.0491 | 1 | 0 | ||||||
| 30 | 68 | I | 2 | 0.0027 | 0.836 | 6.9 | 2 | 0.0109 | 0.528 | 16.67 | ||||||||
| 31 | 69 | I | 1 | 0.0014 | 1 | 1 | 0.0029 | 1 | ||||||||||
| 32 | 74 | D | 11 | 0.0151 | 1 | 0 | 11 | 0.0598 | 1 | |||||||||
| 33 | 80 | D | 1 | 0.0014 | 1 | 1 | 0.0054 | 1 | ||||||||||
| Multi-allelic D′ | 0.9 | 0.86 | 0.96 | 0.87 | ||||||||||||||
I, insertion; D, deletion.