Table 1.
Dimorphic retroelements (absent or present) and STR analysed in this study.
| Retroelement or microsat | Nearest flanking (/) genes | Location within genome reference Ch38/hg38, Chr 6 | Popln frequencies caucasian/Japanese (n = 88–260) | References | |
|---|---|---|---|---|---|
| AluOR | OR12D2 intron | 29396132–29396263 | 0.14 | 0.32 | Kulski et al., 2014 |
| AluOR1 | 3′OR12D1 | 29416044 | Present study | ||
| AluHF | ZFP57/HLA-F | ~29710985* | 0.23 | 0.06 | Dunn et al., 2002 |
| AluHG | HLA-G/HLA-H | ~29850749* | 0.30 | Kulski et al., 2001 | |
| 0.30 | 0.21 | Dunn et al., 2002 | |||
| AluHJ | HLA-J/ETF1P1 | ~30030620* | 0.25 | 0.38 | Dunn et al., 2002 |
| AluTF | MUC21/MUC22 | ~31003947* | 0.11 | 0.08 | Dunn et al., 2003 |
| AluP5 | MICA/MICB | ~31470733* | Present study | ||
| AluMICB | MICB intron 1 | ~31498446* | 0.12 | Kulski et al., 2002a | |
| 0.16 | 0.12 | Kulski and Dunn, 2005 | |||
| HERVK9 | HLA-G/HLA-H | 29875649–29881829 | 0.37 | 0.59 | Kulski et al., 2008 |
| sMER9 (1) | HLA-G/HLA-H | ~29881317* | 0.66 | 0.41 | Kulski et al., 2008 |
| LTR13 | HLA-K/HLA-U | 29929971–29930908 | Present study | ||
| sMER9 (2) | HLA-U/HLA-A | 29936175–29936676 | Kulski et al., 2009 | ||
| LTR5L | TRIM26/HLA-L | ~30221451 | Present study | ||
| MER5/LTR33 | HLA-C/HLA-B | ~31313186 | Present study | ||
| HAL1/MER5A | MICA/MICB | 31418238–31418519 | Present study | ||
| LTR9 | MICA/MICB | 31423445–31424086 | Present study | ||
| SVAOR | 3′GPX6 | 28501515–28503131 | Present study | ||
| SVA-HF | LTR16/HLA-F | 29717873–2972077 | 0.14 | 0.00 | Kulski et al., 2010 |
| SVA-16** | HLA-H/HLA-T | 29895386–29896449 | fixed | Present study | |
| SVA-HA | HLA-K/HLA-A | 29932087–29933753 | 0.26 | 0.06 | Kulski et al., 2010 |
| SVA-T26** | TRIM26/HLA-L | 30221503–30222724 | Present study | ||
| SVA-ER** | MICC/HLA-E | 30474489–30475999 | Present study | ||
| SVA-EG** | HLA-E/GNL1 | 30498159–30499333 | Present study | ||
| SVA-M21** | MUC21/MUC22 | 30992538–30993994 | Present study | ||
| SVA-M22** | MUC22/C6orf15 | 31066602–31068056 | Present study | ||
| SVA-HC | HCG27/HLA-C | 31243860–31245322 | 0.10 | 0.03 | Kulski et al., 2010 |
| SVA-CB | HLA-C/HLA-B | ~31310982* | Present study | ||
| SVA-HB | HLA-C/HLA-B | ~31329940* | 0.65 | 0.25 | Kulski et al., 2010 |
| SVA-MIC | MICA/MICB | 31453745–31456553 | Kulski et al., 2010 | ||
| 9.5-kb del | HLA-C/HLA-B | ~31298645* | Present study | ||
| (ATAG)n | HLA-G/MICF | 29838629–29838750 | Present study | ||
| (CAGAGA)n | HLA-G/MICF | 29838997–29839045 | Present study | ||
| (ATAA)n | HLA-A/HLA-W | 29949553–29949592 | Present study | ||
| (ATTT)n | HLA-A/HLA-W | 29949590–29949639 | Present study | ||
| (TTTA)n | TRIM26/HLA-L | 30221462–30221500 | Present study | ||
| (GAGG)n | MUC22/C60rf15 | ~ 31066254 | Present study | ||
| (TTTC)n | HCG27/HLA-C | 31236405–31236481 | Kulski et al., 1997 | ||
| (ACA)n | HCG27/HLA-C | 31239846–31239880 | Kulski et al., 1997 | ||
| (TTCC)n | HCG27/HLA-C | 31241314–31241352 | Kulski et al., 1997 | ||
| (TTAT)n | HLA-C/HLA-B | 31321185–31321227 | Kulski et al., 1997 | ||
| (CTG)n | within MICA | 31412369–31412393 | Mizuki et al., 1997 | ||
| (TGT)n | within MICA | ~31412394* | Present study | ||
*
Approximate location because these deletions, retroelements or STR are absent from the Ch38/hg38 Genome Reference that has the HLA haplotype of HLA-A*03:01:01:01/ B*07:02:01:01/C*07:02:01:03/.