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

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