Table 2.
Examples of HWE-departure in three ExAC variants.
| Population | Obs:AA | Obs:AB | Obs:BB | Exp:AA | Exp:AB | Exp:BB | MAF | p-HWE | Ratio O/E | d-HWE type |
|---|---|---|---|---|---|---|---|---|---|---|
| C1orf62 (rs7551421): variant located within deletion polymorphism | ||||||||||
| African | 691 | 2,455 | 2,051 | 708 | 2,421 | 2,068 | 0.37 | 0.59 | 1.01 | |
| East Asian | 2,392 | 1,463 | 429 | 2,277 | 1,692 | 314 | 0.73 | 8.4 E-18 | 0.86 | LoH |
| European (Finnish) | 864 | 1,630 | 812 | 853 | 1,653 | 801 | 0.51 | 0.73 | 0.99 | |
| European (Non-Finnish) | 5,564 | 15,393 | 12,372 | 5,276 | 15,969 | 12,084 | 0.40 | 3.8 E-10 | 0.96 | LoH |
| Latino | 1,658 | 2,593 | 1,523 | 1,512 | 2,885 | 1,377 | 0.51 | 1.3 E-13 | 0.90 | LoH |
| South Asian | 2,149 | 3,760 | 2,333 | 1,970 | 4,119 | 2,154 | 0.49 | 2.6 E-14 | 0.91 | LoH |
| C11orf10 (rs509360): variant with strongly different allele frequency across populations | ||||||||||
| African | 3,552 | 1,468 | 173 | 3,537 | 1,497 | 158 | 0.83 | 0.37 | 0.98 | |
| East Asian | 968 | 1,914 | 1,434 | 859 | 2,133 | 1,325 | 0.45 | 1.4 E−10 | 0.90 | LoH |
| European (Finnish) | 416 | 1,503 | 1,380 | 413 | 1,509 | 1,377 | 0.35 | 0.98 | 1.00 | |
| European (Non-Finnish) | 3,423 | 14,518 | 15,378 | 3,425 | 14,515 | 15,380 | 0.32 | 1.00 | 1.00 | |
| Latino | 195 | 1,396 | 4,190 | 138 | 1,510 | 4,133 | 0.15 | 6.8 E−08 | 0.92 | LoH |
| South Asian | 4,205 | 3,292 | 749 | 4,152 | 3,399 | 696 | 0.71 | 0.02 | 0.97 | |
| C1orf31 (rs58896934): variant of deletion-insertion type | ||||||||||
| African | 110 | 1,620 | 2,198 | 215 | 1,409 | 2,303 | 0.23 | 7,6 E−20 | 1.15 | GoH |
| East Asian | 829 | 2,124 | 622 | 1,000 | 1,782 | 793 | 0.53 | 2,0 E−29 | 1.19 | GoH |
| European (Finnish) | 917 | 1,632 | 416 | 1,013 | 1,440 | 512 | 0.58 | 3,8 E−12 | 1.13 | GoH |
| European (Non-Finnish) | 5,685 | 16,989 | 4,949 | 7,279 | 13,802 | 6,543 | 0.51 | 0 | 1.23 | GoH |
| Latino | 531 | 2,895 | 1,412 | 809 | 2,339 | 1,690 | 0.41 | 3.8 E−60 | 1.24 | GoH |
| South Asian | 1,943 | 4,079 | 941 | 2,278 | 3,409 | 1,276 | 0.57 | 4.8 E−59 | 1.20 | GoH |
Obs, Observed genotypes; Exp, expected genotypes under hypothesis of HWE; Ratio O/E, ratio of observed and expected number of heterozygote carriers; p-HWE, p-value of χ2 test for HWE-departure; MAF refers to minor allele frequency as seen in the entire ExAC sample; in some superpopulations this “minor allele” may be the common allele.