Table 1. Minor allele and genotype frequencies of single nucleotide polymorphisms in genes related to the IGF pathway in subcohort members from the Netherlands Cohort Study (1986–2002)a.
| Variant | Gene | Genelocation | Majorallele | Minorallele | MAF | Homozygouscommon genotypeN (%) | Heterozygousgenotype N (%) | Homozygous raregenotype N (%) | P forHWE | Unfavorable alleleas based onliteratureb |
|---|---|---|---|---|---|---|---|---|---|---|
| rs1520220 | IGF1 | 12q23.2 | C | G | 0.18 | 2,292 (67.6) | 989 (29.2) | 110 (3.2) | 0.79 | Minor |
| rs5742678 | IGF1 | 12q23.2 | C | G | 0.25 | 1,921 (56.7) | 1,250 (36.9) | 220 (6.5) | 0.39 | Minor |
| rs5742694 | IGF1 | 12q23.2 | T | G | 0.23 | 2,019 (59.5) | 1,172 (34.6) | 200 (5.9) | 0.09 | Minor |
| rs10735380 | IGF1 | 12q23.2 | A | G | 0.26 | 1,886 (55.6) | 1,271 (37.5) | 234 (6.9) | 0.32 | Minor |
| rs2854744 | IGFBP3 | 7p13-p12 | C | A | 0.45 | 1,002 (29.6) | 1,695 (50.0) | 693 (20.4) | 0.63 | Major |
| rs2132572 | IGFBP3 | 7p13-p12 | G | A | 0.23 | 2,006 (59.2) | 1,198 (35.3) | 187 (5.5) | 0.64 | Minor |
| rs35440925 | IGFBP3 | 7p13-p12 | C | G | 0.21 | 2,110 (62.2) | 1,137 (33.5) | 144 (4.3) | 0.55 | Unclear |
| rs1801278 | IRS1 | 2q36 | G | A | 0.07 | 2,926 (86.3) | 450 (13.3) | 15 (0.4) | 0.60 | Minor |
| rs1805097 | IRS2 | 13q34 | G | A | 0.35 | 1,431 (42.4) | 1,530 (45.3) | 416 (12.3) | 0.82 | Major |
| rs2289046 | IRS2 | 13q34 | A | G | 0.34 | 1,466 (43.2) | 1,538 (45.4) | 387 (11.4) | 0.59 | Major |
| rs754204 | IRS2 | 13q34 | C | T | 0.48 | 906 (27.2) | 1,689 (50.6) | 740 (22.2) | 0.37 | Minor |
| rs4773082 | IRS2 | 13q34 | T | C | 0.43 | 994 (32.2) | 1,518 (49.1) | 578 (18.7) | 0.97 | Minor |
| rs4988496 | GHRHR | 7p14 | G | A | 0.06 | 3,008 (88.7) | 371 (10.9) | 11 (0.3) | 0.90 | Minor |
| rs1801282 | PPARG | 3p25 | C | G | 0.12 | 2,607 (76.9) | 739 (21.8) | 43 (1.3) | 0.25 | Major |
| rs1501299 | ADIPOQ | 3q27 | C | A | 0.26 | 1,852 (54.6) | 1,290 (38.0) | 249 (7.3) | 0.24 | Major |
| rs2241766 | ADIPOQ | 3q27 | T | G | 0.12 | 2,630 (77.9) | 707 (21.0) | 38 (1.1) | 0.21 | Unclear |
| rs266729 | ADIPOQ | 3q27 | C | G | 0.26 | 1,860 (54.9) | 1,300 (38.3) | 231 (6.8) | 0.85 | Major |
| rs1648707 | ADIPOQ | 3q27 | A | C | 0.33 | 1,526 (45.0) | 1,500 (44.2) | 365 (10.8) | 0.90 | Minor |
| rs182052 | ADIPOQ | 3q27 | G | A | 0.33 | 1,519 (44.8) | 1,501 (44.3) | 371 (10.9) | 0.99 | Unclear |
| rs1342387 | ADIPOR1 | 1q32.1 | G | A | 0.45 | 986 (29.1) | 1,744 (51.5) | 660 (19.5) | 0.02 | Major |
| rs7539542 | ADIPOR1 | 1q32.1 | C | G | 0.30 | 1,637 (48.4) | 1,440 (42.6) | 305 (9.0) | 0.65 | Unclear |
| rs12733285 | ADIPOR1 | 1q32.1 | C | T | 0.29 | 1,707 (50.4) | 1,418 (41.9) | 260 (7.7) | 0.14 | Major |
| rs1044471 | ADIPOR2 | 12p13.31 | C | T | 0.46 | 981 (29.0) | 1,681 (49.7) | 723 (21.4) | 0.95 | Unclear |
| rs767870 | ADIPOR2 | 12p13.31 | T | C | 0.18 | 2,280 (67.3) | 1,013 (29.9) | 97 (2.9) | 0.22 | Unclear |
Abbreviations: ADIPOQ, adiponectin; ADIPOR1 and -2, adiponectin receptor 1 and 2; GHRHR, growth hormone releasing hormone receptor; HWE, Hardy-Weinberg equilibrium; IGF, insulin-like growth factor; IGF1, insulin-like growth factor 1; IGFBP3, insulin-like growth factor binding protein 3; IRS1 and -2, insulin receptor substrate 1 and 2; MAF, minor allele frequency; N, number of; PPARG, peroxisome proliferator-activated receptor gamma
aFrequencies are presented for men and women together because none of these germline genetic variants were located on sex chromosomes.
bA reference list on the basis of which the unfavorable allele was defined is included in the Supplementary Table 1.