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Table 1 Summary of INDELs and VNTRs that have been studied for association with common polygenic obesity and its related traits and complications

From: The association of insertions/deletions (INDELs) and variable number tandem repeats (VNTRs) with 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