Table S1.
Minor allele frequencies (MAF) of 211 tagging single nucleotide polymorphisms (SNPs) in the Xhosa and Cape Mixed Ancestry (CMA) populations
| MAF | HWE p value | ||||||
|---|---|---|---|---|---|---|---|
| Gene | SNP | Minor allele | Call rate | CMA | Xhosa | CMA | Xhosa |
| ABCB1 | rs2229109 | A | 1 | 0.0 | 0.0 | NA | NA |
| ABCB1 | rs1202185 | G | 1 | 0.187 | 0.216 | 0.789 | 0.242 |
| ABCB1 | rs10233247 | G | 1 | 0.075 | 0.101 | 2.22E-16 | 0.0 |
| ABCB1 | rs2235046 | A | 1 | 0.254 | 0.211 | 0.84 | 0.624 |
| ABCB1 | rs4148743 | A | 1 | 0.41 | 0.358 | 0.248 | 0.691 |
| ABCB1 | rs2373589 | A | 1 | 0.373 | 0.339 | 0.0551 | 0.297 |
| ABCB1 | rs6946119 | G | 1 | 0.067 | 0.041 | 0.556 | 0.653 |
| ABCB1 | rs10275831 | A | 1 | 0.037 | 0.05 | 0.751 | 0.579 |
| ABCB1 | rs1858923 | G | 1 | 0.239 | 0.128 | 0.428 | 0.863 |
| ABCB1 | rs2235033 | G | 1 | 0.463 | 0.472 | 0.25 | 0.898 |
| ABCB1 | rs2157926 | T | 1 | 0.537 | 0.413 | 0.0328 | 0.574 |
| ABCB1 | rs1922242 | T | 1 | 0.448 | 0.491 | 0.779 | 0.629 |
| ABCB1 | rs2032588 | A | 1 | 0.127 | 0.197 | 0.931 | 0.453 |
| ABCB1 | rs10267099 | G | 1 | 0.09 | 0.11 | 0.421 | 0.197 |
| ABCB1 | rs7787082 | G | 1 | 0.396 | 0.317 | 0.0048 | 0.0708 |
| ABCB1 | rs4148740 | G | 1 | 0.179 | 0.142 | 0.48 | 0.532 |
| ABCB1 | rs1211152 | A | 1 | 0.0 | 0.0 | NA | NA |
| ABCB1 | rs7796247 | A | 1 | 0.037 | 0.05 | 0.751 | 0.579 |
| ABCB1 | rs1202175 | G | 1 | 0.187 | 0.216 | 0.789 | 0.242 |
| ABCB1 | rs1922241 | A | 1 | 0.216 | 0.193 | 0.535 | 0.52 |
| ABCB1 | rs6465118 | A | 1 | 0.224 | 0.229 | 0.652 | 0.493 |
| ABCB1 | rs4728705 | A | 1 | 0.134 | 0.133 | 0.826 | 0.44 |
| ABCB1 | rs13229143 | G | 1 | 0.239 | 0.124 | 0.428 | 0.772 |
| ABCB1 | rs6950978 | T | 1 | 0.0 | 0.0 | NA | NA |
| ABCB1 | rs1202172 | C | 1 | 0.351 | 0.362 | 0.505 | 0.776 |
| ABCB1 | rs4148732 | G | 1 | 0.0 | 0.0 | NA | NA |
| ABCB1 | rs10274587 | A | 1 | 0.134 | 0.128 | 0.826 | 0.304 |
| ABCB1 | rs3789243 | A | 1 | 0.396 | 0.372 | 0.205 | 0.0968 |
| ABCB1 | rs4437575 | G | 1 | 0.418 | 0.353 | 0.881 | 0.557 |
| ABCB1 | rs4728709 | G | 1 | 0.522 | 0.408 | 0.108 | 0.261 |
| ABCB1 | rs4728707 | A | 1 | 0.209 | 0.188 | 0.0306 | 0.928 |
| ABCB1 | rs2032583 | G | 1 | 0.187 | 0.147 | 0.591 | 0.618 |
| ABCB1 | rs17149866 | G | 1 | 0.03 | 0.028 | 2.22E-16 | 0.0 |
| ABCB1 | rs1882479 | G | 1 | 0.119 | 0.106 | 0.959 | 0.0698 |
| ABCB1 | rs1055302 | A | 1 | 0.231 | 0.33 | 0.687 | 0.211 |
| ABCB1 | rs12334183 | G | 1 | 0.246 | 0.317 | 0.202 | 0.395 |
| ABCB1 | rs10264990 | G | 1 | 0.299 | 0.275 | 0.25 | 0.902 |
| ABCB1 | rs17149699 | A | 1 | 0.284 | 0.321 | 0.713 | 0.917 |
| ABCB1 | rs1882478 | G | 1 | 0.425 | 0.399 | 0.289 | 0.0243 |
| ABCB1 | rs10248420 | A | 1 | 0.448 | 0.413 | 0.00595 | 0.339 |
| ABCB1 | rs10236274 | G | 1 | 0.254 | 0.289 | 0.136 | 0.327 |
| ABCB1 | rs3213619 | G | 1 | 0.224 | 0.193 | 0.652 | 0.977 |
| ABCB1 | rs10225473 | G | 1 | 0.127 | 0.119 | 0.931 | 0.186 |
| ABCB1 | rs17327442 | A | 1 | 0.478 | 0.459 | 2.22E-16 | 0.0 |
| ABCB1 | rs17149792 | A | 1 | 0.119 | 0.266 | 0.959 | 0.529 |
| ABCB1 | rs1202169 | G | 1 | 0.261 | 0.225 | 0.718 | 0.781 |
| ABCB1 | rs6949448 | A | 1 | 0.187 | 0.151 | 0.591 | 0.708 |
| ABCB1 | rs1202184 | A | 1 | 0.269 | 0.106 | 0.919 | 0.218 |
| ABCB1 | rs4148745 | A | 1 | 0.127 | 0.138 | 0.309 | 0.39 |
| ABCB1 | rs1002205 | C | 0.994 | 0.276 | 0.292 | 0.947 | 0.025 |
| ABCB1 | rs17327624 | A | 0.994 | 0.209 | 0.185 | 0.956 | 0.85 |
| ABCB1 | rs1202181 | G | 0.994 | 0.187 | 0.213 | 0.789 | 0.276 |
| ABCB1 | rs2235023 | A | 0.994 | 0.269 | 0.333 | 0.919 | 1.0 |
| ABCB1 | rs4148734 | A | 0.994 | 0.067 | 0.032 | 0.174 | 0.728 |
| ABCB1 | rs13233308 | A | 0.994 | 0.182 | 0.018 | 0.328 | 0.845 |
| ABCB1 | rs1045642 | T | 0.994 | 0.205 | 0.11 | 0.349 | 0.754 |
| ABCB1 | rs4148738 | G | 0.989 | 0.194 | 0.164 | 0.683 | 0.922 |
| ABCB1 | rs7779562 | G | 0.983 | 0.4 | 0.444 | 0.179 | 0.153 |
| ABCB1 | rs9282564 | G | 0.977 | 0.008 | 0.0 | 0.95 | NA |
| ABCB1 | rs10808071 | G | 0.977 | 0.164 | 0.194 | 0.0379 | 0.0732 |
| ABCB1 | rs2235041 | A | 0.977 | 0.077 | 0.126 | 0.282 | 0.256 |
| ABCB1 | rs2235074 | NA | 0.665 | NA | NA | NA | NA |
| ABCB1 | rs1002204 | NA | 0.119 | NA | NA | NA | NA |
| ABCC2 | rs2073337 | G | 1 | 0.403 | 0.491 | 0.34 | 0.387 |
| ABCC2 | rs7476245 | A | 1 | 0.097 | 0.092 | 0.606 | 0.0167 |
| ABCC2 | rs8187707 | A | 1 | 0.082 | 0.083 | 0.374 | 0.347 |
| ABCC2 | rs17216282 | G | 1 | 0.194 | 0.161 | 0.248 | 0.198 |
| ABCC2 | rs8187674 | G | 1 | 0.045 | 0.055 | 0.701 | 0.543 |
| ABCC2 | rs2180989 | C | 1 | 0.276 | 0.317 | 0.586 | 0.684 |
| ABCC2 | rs11595888 | A | 1 | 0.0 | 0.0 | NA | NA |
| ABCC2 | rs4148396 | A | 1 | 0.321 | 0.303 | 0.537 | 0.997 |
| ABCC2 | rs4148399 | C | 1 | 0.045 | 0.133 | 0.701 | 0.44 |
| ABCC2 | rs4148398 | A | 1 | 0.187 | 0.101 | 0.591 | 0.907 |
| ABCC2 | rs17112266 | A | 1 | 0.052 | 0.078 | 0.652 | 0.377 |
| ABCC2 | rs7067971 | G | 1 | 0.201 | 0.138 | 0.832 | 0.39 |
| ABCC2 | rs2804398 | A | 1 | 0.269 | 0.317 | 0.469 | 0.684 |
| ABCC2 | rs3740065 | G | 1 | 0.313 | 0.445 | 0.812 | 0.822 |
| ABCC2 | rs3740063 | A | 1 | 0.5 | 0.477 | 0.903 | 0.647 |
| ABCC2 | rs2273697 | A | 1 | 0.187 | 0.11 | 0.591 | 0.101 |
| ABCC2 | rs7898096 | A | 1 | 0.09 | 0.211 | 0.421 | 0.0702 |
| ABCC2 | rs2002042 | A | 0.994 | 0.201 | 0.185 | 0.832 | 0.408 |
| ABCC2 | rs2756109 | A | 0.983 | 0.47 | 0.448 | 0.691 | 0.779 |
| ABCC2 | rs4148391 | T | 0.977 | 0.0 | 0.0 | NA | NA |
| ABCC2 | rs717620 | T | 0.898 | 0.04 | 0.037 | 0.743 | 0.709 |
| ABCC2 | rs8187710 | NA | 0.341 | NA | NA | NA | NA |
| ABCC2 | rs2756112 | NA | 0 | NA | NA | NA | NA |
| CYP2A7P1 | rs7250597 | A | 1 | 0.082 | 0.165 | 0.464 | 0.499 |
| CYP2A7P1 | rs7249735 | C | 1 | 0.06 | 0.092 | 2.22E-16 | 0.0 |
| CYP2A7P1 | rs7255146 | A | 0.994 | 0.227 | 0.339 | 0.774 | 0.128 |
| CYP2A7P1 | rs11666982 | A | 0.994 | 0.433 | 0.227 | 0.471 | 0.161 |
| CYP2B6 | rs1042389 | G | 1 | 0.231 | 0.271 | 0.0138 | 0.633 |
| CYP2B6 | rs8192719 | A | 1 | 0.306 | 0.317 | 0.464 | 0.0294 |
| CYP2B6 | rs28399499 | G | 1 | 0.09 | 0.174 | 2.22E-16 | 0.0 |
| CYP2B6 | rs35773040 | A | 1 | 0.0 | 0.0 | NA | NA |
| CYP2B6 | rs35303484 | G | 1 | 0.0 | 0.0 | NA | NA |
| CYP2B6 | rs2279345 | A | 1 | 0.216 | 0.161 | 0.18 | 0.398 |
| CYP2B6 | rs7260329 | A | 1 | 0.209 | 0.106 | 0.956 | 0.218 |
| CYP2B6 | rs3211371 | G | 1 | 0.0 | 0.0 | NA | NA |
| CYP2B6 | rs16974799 | A | 1 | 0.306 | 0.335 | 0.464 | 0.0694 |
| CYP2B6 | rs7255374 | A | 1 | 0.366 | 0.399 | 0.614 | 0.18 |
| CYP2B6 | rs36060847 | A | 1 | 0.0 | 0.0 | NA | NA |
| CYP2B6 | rs8100458 | G | 1 | 0.336 | 0.252 | 0.394 | 0.136 |
| CYP2B6 | rs2113103 | A | 1 | 0.261 | 0.151 | 0.104 | 0.0626 |
| CYP2B6 | rs35979566 | A | 1 | 0.0 | 0.0 | NA | NA |
| CYP2B6 | rs36079186 | G | 1 | 0.0 | 0.0 | NA | NA |
| CYP2B6 | rs34223104 | G | 1 | 0.007 | 0.005 | 0.951 | 0.962 |
| CYP2B6 | rs2279342 | A | 1 | 0.015 | 0.018 | 0.901 | 0.845 |
| CYP2B6 | rs8192712 | G | 1 | 0.03 | 0.009 | 0.801 | 0.923 |
| CYP2B6 | rs2054675 | G | 1 | 0.306 | 0.339 | 0.464 | 0.0514 |
| CYP2B6 | rs3745274 | C | 1 | 0.231 | 0.202 | 0.0138 | 0.00829 |
| CYP2B6 | rs11882450 | G | 0.994 | 0.06 | 0.079 | 0.603 | 0.66 |
| CYP2B6 | rs4803417 | C | 0.994 | 0.159 | 0.115 | 0.0321 | 0.683 |
| CYP2B6 | rs6508963 | A | 0.994 | 0.007 | 0.023 | 0.951 | 0.805 |
| CYP2B6 | rs34097093 | A | 0.983 | 0.0 | 0.0 | NA | NA |
| CYP2B6 | rs2306606 | G | 0.983 | 0.201 | 0.184 | 0.0389 | 0.0203 |
| CYP2B6 | rs2279343 | NA | 0 | NA | NA | NA | NA |
| CYP2C18 | rs11188059 | A | 1 | 0.03 | 0.0 | 0.801 | NA |
| CYP2C18 | rs932809 | A | 1 | 0.224 | 0.248 | 0.801 | 0.5 |
| CYP2C18 | rs12243416 | A | 1 | 0.09 | 0.151 | 0.421 | 0.711 |
| CYP2C18 | rs1326830 | A | 1 | 0.067 | 0.0 | 0.174 | NA |
| CYP2C18 | rs7896133 | A | 1 | 0.201 | 0.202 | 0.832 | 0.128 |
| CYP2C18 | rs2296680 | A | 1 | 0.209 | 0.234 | 0.956 | 0.277 |
| CYP2C18 | rs2296684 | A | 1 | 0.067 | 0.119 | 0.174 | 0.682 |
| CYP2C18 | rs2860840 | A | 1 | 0.09 | 0.005 | 0.421 | 0.962 |
| CYP2C18 | rs10509675 | A | 1 | 0.09 | 0.151 | 0.421 | 0.711 |
| CYP2C18 | rs1409656 | G | 1 | 0.112 | 0.151 | 0.302 | 0.708 |
| CYP2C18 | rs7917985 | A | 1 | 0.157 | 0.266 | 0.551 | 0.889 |
| CYP2C18 | rs7085563 | A | 0.994 | 0.333 | 0.404 | 0.0648 | 0.0581 |
| CYP2C18 | rs1010570 | A | 0.994 | 0.485 | 0.495 | 0.114 | 0.564 |
| CYP2C18 | rs1409655 | A | 0.994 | 0.098 | 0.064 | 0.375 | 0.38 |
| CYP2C18 | rs11188067 | G | 0.983 | 0.1 | 0.148 | 0.37 | 0.778 |
| CYP2C19 | rs10509677 | G | 1 | 0.022 | 0.014 | 0.851 | 0.884 |
| CYP2C19 | rs4917623 | G | 1 | 0.209 | 0.115 | 0.427 | 0.683 |
| CYP2C19 | rs1322179 | A | 1 | 0.201 | 0.211 | 0.832 | 0.509 |
| CYP2C19 | rs12248560 | A | 1 | 0.09 | 0.151 | 0.421 | 0.711 |
| CYP2C19 | rs4244285 | A | 1 | 0.201 | 0.22 | 0.832 | 0.339 |
| CYP2C19 | rs7101258 | C | 1 | 0.172 | 0.183 | 0.378 | 0.395 |
| CYP2C19 | rs7915414 | A | 0.994 | 0.418 | 0.44 | 0.0309 | 0.966 |
| CYP2D6 | rs5758589 | A | 1 | 0.321 | 0.335 | 0.537 | 0.339 |
| CYP2D6 | rs9623531 | G | 0.983 | 0.408 | 0.338 | 0.259 | 0.151 |
| CYP3A4 | rs4986910 | G | 1 | 0.0 | 0.0 | NA | NA |
| CYP3A4 | rs28371759 | G | 1 | 0.0 | 0.0 | NA | NA |
| CYP3A4 | rs17161829 | A | 1 | 0.09 | 0.22 | 0.421 | 0.0669 |
| CYP3A4 | rs7801671 | C | 1 | 0.328 | 0.284 | 6.29E-05 | 3.33E-05 |
| CYP3A4 | rs17161886 | C | 1 | 0.104 | 0.252 | 0.34 | 0.0455 |
| CYP3A4 | rs2687117 | A | 1 | 0.172 | 0.275 | 0.403 | 0.721 |
| CYP3A4 | rs12333983 | A | 1 | 0.433 | 0.271 | 0.471 | 0.328 |
| CYP3A4 | rs2740574 | A | 1 | 0.425 | 0.234 | 0.575 | 0.606 |
| CYP3A4 | rs4986909 | A | 1 | 0.0 | 0.0 | NA | NA |
| CYP3A4 | rs2738258 | A | 1 | 0.172 | 0.358 | 0.00932 | 0.691 |
| CYP3A4 | rs10267228 | C | 0.994 | 0.306 | 0.333 | 0.676 | 0.0833 |
| CYP3A4 | rs7811025 | A | 0.983 | 0.159 | 0.341 | 1.54E-11 | 0 |
| CYP3A4 | rs4987161 | G | 0.983 | 0.0 | 0.0 | NA | NA |
| CYP3A5 | rs4646450 | C | 1 | 0.172 | 0.032 | 0.0817 | 5.98E-09 |
| CYP3A5 | rs1419745 | G | 1 | 0.433 | 0.495 | 0.00671 | 0.773 |
| CYP3A5 | rs4646446 | A | 1 | 0.104 | 0.046 | 0.34 | 0.616 |
| CYP3A5 | rs10224569 | A | 0.994 | 0.194 | 0.329 | 0.248 | 0.309 |
| CYP3A5 | rs10264272 | A | 0.989 | 0.179 | 0.201 | 0.48 | 0.427 |
| CYP3A7 | rs10211 | A | 1 | 0.522 | 0.358 | 0.00101 | 0.663 |
| CYP3A7 | rs2687144 | A | 1 | 0.53 | 0.431 | 0.0024 | 0.774 |
| CYP3A7 | rs2687074 | C | 1 | 0.164 | 0.252 | 0.0508 | 0.295 |
| CYP3A7 | rs2687136 | A | 0.994 | 0.508 | 0.463 | 0.0139 | 0.191 |
| SLC22A6 | rs12293966 | G | 1 | 0.082 | 0.193 | 0.464 | 0.977 |
| SLC22A6 | rs6591722 | A | 1 | 0.149 | 0.083 | 0.0158 | 0.112 |
| SLC22A6 | rs2276300 | A | 1 | 0.0 | 0.0 | NA | NA |
| SLC22A6 | rs4149170 | A | 1 | 0.284 | 0.45 | 0.404 | 0.691 |
| SLC22A6 | rs955434 | A | 0.994 | 0.22 | 0.234 | 0.894 | 0.985 |
| SLC22A6 | rs10897310 | NA | 0.591 | NA | NA | NA | NA |
| UGT1A1 | rs4663972 | G | 1 | 0.239 | 0.431 | 0.143 | 0.621 |
| UGT1A1 | rs28900396 | G | 1 | 0.149 | 0.339 | 0.625 | 0.142 |
| UGT1A1 | rs4148323 | A | 1 | 0 | 0 | NA | NA |
| UGT1A1 | rs3755319 | A | 1 | 0.396 | 0.261 | 0.806 | 0.823 |
| UGT1A1 | rs10199882 | G | 1 | 0.164 | 0.156 | 0.288 | 0.326 |
| UGT1A1 | rs11563251 | G | 1 | 0.56 | 0.44 | 0.996 | 0.469 |
| UGT1A1 | rs1018124 | G | 1 | 0.09 | 0.087 | 0.421 | 0.836 |
| UGT1A1 | rs4148328 | A | 1 | 0.269 | 0.124 | 0.469 | 0.14 |
| UGT1A1 | rs9784064 | A | 1 | 0.119 | 0.197 | 0.267 | 0.0103 |
| UGT1A1 | rs10929303 | A | 1 | 0.299 | 0.381 | 0.0771 | 0.465 |
| UGT1A1 | rs887829 | A | 1 | 0.366 | 0.353 | 0.109 | 0.503 |
| UGT1A1 | rs4148329 | A | 1 | 0.418 | 0.216 | 0.393 | 0.242 |
| UGT1A1 | rs2003569 | A | 1 | 0.209 | 0.367 | 0.125 | 0.269 |
| UGT1A1 | rs7572563 | G | 1 | 0.328 | 0.147 | 0.0741 | 0.0725 |
| UGT1A1 | rs3771342 | A | 1 | 0.164 | 0.165 | 0.00446 | 0.475 |
| UGT1A1 | rs8330 | C | 1 | 0.276 | 0.385 | 0.586 | 0.0907 |
| UGT1A1 | rs28946889 | A | 0.994 | 0.0 | 0.0 | NA | NA |
| UGT1A1 | rs929596 | G | 0.994 | 0.333 | 0.312 | 0.14 | 0.0398 |
| UGT1A1 | rs1500482 | G | 0.994 | 0.144 | 0.193 | 0.527 | 0.208 |
| UGT1A1 | rs4663971 | C | 0.983 | 0.469 | 0.477 | 0.4 | 0.184 |
| UGT1A1 | rs6431630 | NA | 0 | NA | NA | NA | NA |
Abbreviations: Call rate, percentage of samples with a genotype; HWE, Hardy-Weinberg equilibrium; NA, no data available
*Grey boxes indicate SNPs with call rates < 90 per cent