Table 1.
Nonreference HML-2 insertions in human genomes
| Locus | Coordinate GRCh37/hg19 | Alias* | Alleles† | Flanking region and other properties | First report in humans (source) |
| 1p13.2‡ | chr1:111,802,592 | De5;K1 | LTR, pre | L1 (L1PA6) | (41) |
| 1p21.1‡ | chr1:106,015,875 | LTR, pre | (12) | ||
| 1p31.1c | chr1:79,792,629 | LTR, pre | AluSz | This study | |
| 1q41 | chr1:223,578,304 | K2 | LTR, pre | L1 (L1MDa) | (12) |
| 3q11.2 | chr3:94,943,488 | LTR, pre | L1 (L1PA10) | This study | |
| 4p16c | chr4:9,603,240 | K6 | LTR, pre | ERV1 (HERVS71) | (12) |
| 4p16d | chr4:9,981,605 | LTR, pre | L2 L2b; SLCA29 intron 5/6 | This study | |
| 5p15.32 | chr5:4,537,604 | LTR, pre | ERV1 (LTR1C) | This study | |
| 5q12.3 | chr5:64,388,440 | Ne7;K12 | LTR, pre | L1 L1M6 | (12) |
| 5q14.1 | chr5:80,442,266 | De6/Ne1;K10 | LTR, pre | RASGRF2 intron 17 | (12) |
| 6p21.32 | chr6:32,648,036 | LTR, pre | L1 (L1PA10) | (12) | |
| 6p22.3 | chr6:16,004,859 | LTR, pre | AluSx | This study | |
| 6q26 | chr6:161,270,899 | De2;K12 | LTR, pre | (12) | |
| 7q36.3 | chr7:158,773,385 | LTR, pre | This study | ||
| 8q24.3c | chr8:146,086,169 | pro, pre | ERV1 (LTR46); COMMD5 intron 9 of transcript variant 2; gag and pro ORFs | This study | |
| 10q24.2b | chr10:101,016,122 | De12 | ERL MalR (MSTD); unexpected structure | This study | |
| 10q26.3§ | chr10:134,444,012 | LTR, pre | INPP5A intron 2 | This study | |
| 11q12.2 | chr11:60,449,890 | De4;K18 | LTR, pre | L1 (L1M4); LINC00301 intron 6 | (12) |
| 12q12 | chr12:44,313,657 | Ne6;K20 | LTR, pre | L1 (L1MB1); TMEM117 intron 2 | (12) |
| 12q24.31 | chr12:124,066,477 | K21 | LTR, pre | AluSx1; LOC101927415 exon 3 | (12) |
| 12q24.32§ | chr12:127,638,080–127,639,871 | LTR, pre | ERV1 (MER57); deleted in hg19; from fosmid CloneDB: AC195745.1 bases 17648–18615 | (43) | |
| 13q31.3 | chr13:90,743,183 | Ne2;K22 | LTR, pre | SINE (FLAM_A); LINC0559 intron 3 | (12) |
| 15q13.1 | chr15:28,430,088 | HERC2 intron 56; unexpected structure | This study | ||
| 15q22.2 | chr15:63,374,594 | K24 | LTR, pre | (12) | |
| 19p12b | chr19:21,841,536 | De1;K113 | pro, pre | (9) | |
| 19p12d | chr19:22,414,379 | pro, pre | Deletion in 5′ LTR; pro ORF; insertion within fosmid clone accession AC245253.1 | (41) | |
| 19p12e | chr19:22,457,244 | De11 | pro, pre | AluSq | This study |
| 19q12§ | chr19:29,855,781 | De3;K28 | LTR, pre | LOC284395 intron 9 | (12) |
| 19q13.43 | chr19:57,996,939 | Ne5 | LTR, pre | 2 kb upstream of ZNF419 | This study |
| 20p12.1 | chr20:12,402,387 | De14*;K30 | LTR, pre | (12) | |
| 22q11.23b§ | chr22:23852639–23852640 | De7;K16 | LTR, pre | ERVL-MalR (MLT1C); maps to Hg38 alt locus scaffold 22_KI270878v1_alt:156355–180653 | This study |
| Xq21.33 | chrX:93,606,603 | De9 | pro, pre | L1 (L1MD1); gag, prol, pol, env ORFs | This study |
| Dup 1§ | Not determined | LTR | Flank maps to centromere associated duplications on multiple chromosomes | This study | |
| Dup 2§ | Not determined | LTR, pre | Flank maps to duplicated regions within predicted FAM86 and ALG1L2 exonic variants | This study | |
| Dup 3§ | Not determined | LTR, pre | Flank maps to 3 segmental duplications on chr1 | This study | |
| Dup 4§ | Not determined | LTR, pre | Deletion in hg19 reference; putative empty site on chr19 within fosmid CloneDB: AC232224.2 | This study |
*
Reported originally in the sequenced Neandertal (Ne) or Denisovan (De) by Agoni et al. (42) or Lee et al. (51), or in modern humans (K) by Marchi et al. (12) or Lee et al. (41).
†
Alleles detected. LTR, solo LTR; pre, preinsertion site; pro, 2-LTR provirus.
‡
Previously PCR validated as solo-LTR by Lee et al. (41).
§
Insertion is located within an encompassing structural variant not present in the hg19 reference.