Table 1.
Summary of INDELs and VNTRs that have been studied for association with common polygenic obesity and its related traits and complications
| Gene/nearest gene | INDEL/VNTR | Type(s) [pivotal reference] | Location in human chromosome |
|---|---|---|---|
| FTO | INDELs | 13 insertions and 27 deletions (1–9 bp)—16 known in dbSNP and 24 potentially novel [37] | hg18, chr16: 52307514–52699069 |
| LEP | VNTR | (CTTT)n
Type 1 allele: 121–145 [49] or 146–178 bp [51] Type 2 allele: 197–225 [49] or 165–193 bp [51] Type 3 allele: 210–254 bp [51] |
3912 bp 3′ of the LEP stop codon (476 bp 3′ of the 3′ UTR) |
| LEPR | STR/VNTR | D1S200: (CA)n; 13–27 repeats; 17 most common [56, 57] | UniSTS: 56325; Chr1 c.77.73 cM |
| D1S3728 [58] | UniSTS: 56029; Chr1 c.89.49 cM | ||
| D1S1665 [58] | UniSTS: 60783; Chr1 c.99.62 cM | ||
| (CA)n [59] | Intron 3 of LEPR | ||
| (CTTT)n [59] | Intron 16 of LEPR | ||
| INDEL | CTTTA [60] | 3′ UTR of LEPR | |
| TAT [61] | 1078Y codon of LEPR | ||
| POMC | STR/VNTR | D2S1788: (GATA)n; 4–20 repeats; 15 most common [62, 63] | UniSTS: 6210; Chr2 55.51 cM |
| D2S2170 [55] | UniSTS: 60770; Chr2 47.98 cM | ||
| D2S144 [55] | UniSTS: 68025; Chr2 45.3 cM | ||
| D2S1268 [55] | UniSTS: 149288; Chr2 | ||
| D2S1348 [55] | UniSTS: 54913; Chr2 | ||
| D2S2221 [68] | UniSTS: 32562; Chr2 46.54 cM | ||
| D2S171 [68] | UniSTS: 73301; Chr2 149.4 cr3000 | ||
| D2S2337 [68] | UniSTS: 14003; Chr2 47.76 cM | ||
| INDEL | Trinucleotide repeat (9 bp) [69] | Exon 3 of POMC (codon 94) | |
| MC4R | STR/VNTR | D18S851 [81] | UniSTS: 39301; Chr18 382.9 cr3000 |
| D18S487 [81] | UniSTS: 84391; Chr18 20924 cr50000 | ||
| D18S69 [81] | UniSTS: 47737; Chr18 2049 cr10000 | ||
| D18S858 [81]; 8–20 repeats; 11/12 most common [57] | UniSTS: 14041; Chr18 80.41 cM | ||
| D18S849 [81] | UniSTS: 15592; Chr18 430.2 cr3000 | ||
| D18S1155 [81] | UniSTS: 32047; Chr18 81.27 cM | ||
| D18S64 [81] | UniSTS: 17561; Chr18 84.8 cM | ||
| D18S38 [81] | UniSTS: 14742; Chr18 84.98 cM | ||
| UCP2 | STR/VNTR | D11S912 [4, 57, 81] | UniSTS: 72663; Chr11 137.93 cM |
| INDEL | 45 bp [88] | 3′ UTR of UCP2 exon 8 | |
| SLC6A4/5HTT | VNTR | 5-HTTLPR 43 bp; 14R (short, S) and 16R (long, L) alleles [102] | 1 kb upstream of the SLC6A4/5HTT transcription start site |
| STin2 17 bp; common 10- and 12-repeat alleles and a rare 9-repeat allele [103, 104] | Intron 2 of SLC6A4/5HTT | ||
| SLC6A3/DAT1 | VNTR | 40 bp; 9-repeat (S) and 10-repeat (L) alleles [118] | 3′ UTR of SLC6A3/DAT1 |
| DRD2 | INDEL | 1 bp; dbSNP rs1799732; -141C [121] | 5′ UTR of DRD2 |
| DRD4 | VNTR | 48 bp; 2–10 repeats; 4-repeat (4R or S) and 7-repeat (7R or L) alleles most common [132] | Exon 3 of DRD4 |
| MAOA | VNTR | 30 bp; 2-, 3-, 3.5-, 4-, 5-, or 6-repeat copies [151]; 3- and 4-repeat alleles most common [146] | Promoter region of MAOA |
| TH | VNTR | (TCAT)n; T6, T7, T8, T9, and T10 alleles [157] | Intron 1 of TH |
| INS | VNTR | 14–15 bp; short class I allele (~570 bp, 26–63 repeats), class II alleles (~1320 bp, about 80 repeats), and the long class III (~2470, 141–209 repeats) [167] | 63 bp from the INS transcription starting site (promoter region) |
| IL1RA | VNTR | 86 bp; 1, 2, 3, 4, 5, and 6 repeats; 4-repeat (allele I) and 2-repeat (allele II) most common [196] | Intron 2 of IL1RA |
| IL4 | VNTR | 70 bp; 2-repeat (B1) and 3-repeat (B2) alleles most common [209] | Intron 3 of IL4 |
| eNOS/NOS3 | VNTR | 27 bp; 4-repeat (a) and 5-repeat (b) alleles most common [223] | Intron 4 of eNOS/NOS3 |
| ACE | INDEL | 287 bp; dbSNP rs1799752 [241] | Intron 16 of ACE |
| DOCK5 | VNTR | VNTR A; 590–640-bp allele [261] | chr8: 25085372–25085875; ~12 kb upstream of DOCK5 |
| VNTR B; 944–1022-, 1112–1127-, 1073–1084-, and 1099–1103-bp alleles [261] | chr8: 25129579–25130501; intron 1 of DOCK5 | ||
| INDEL | 3975 bp [261] | chr8: 25122602–25126576; intron 1 of DOCK5 | |
| PER3 | VNTR | 54 bp; 4-repeat and 5-repeat alleles [262] | Exon 18 of PER3 |