Table 1.
Allele frequencies in AGVP and KGP African populations of variants previously detected to be under selection (west African in blue, southern African in green, east African in pink and non-African in yellow)
| Gene | SNP ID | DA | GWD | MSL | ESN | YRI | ZUL | LWK | BAG | ETH | CEU | CHB |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Lactase Persistence | ||||||||||||
| MCM6 | rs145946881 | G | 0.000 | 0.000 | 0.000 | 0.000 | 0.070 | 0.086 | 0.075 | 0.000 | 0.000 | 0.000 |
| MCM6 | rs41380347 | C | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.017 | 0.000 | 0.000 |
| MCM6 | rs41525747 | C | NA | NA | NA | NA | 0.000 | NA | 0.000 | 0.050 | NA | NA |
| MCM6 | rs4954490 | A | 0.128 | 0.088 | 0.116 | 0.056 | 0.105 | 0.126 | 0.110 | 0.258 | 0.798 | 0.340 |
| MCM6 | rs4988235 | A | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.058 | 0.737 | 0.000 |
| MCM6 | rs869051967 | C | NA | NA | NA | NA | 0.000 | NA | 0.000 | 0.008 | NA | NA |
| Malaria | ||||||||||||
| CD36 | rs3211938 | G | 0.009 | 0.006 | 0.242 | 0.292 | 0.005 | 0.076 | 0.050 | 0.000 | 0.000 | 0.000 |
| DARC | rs12075 | G | 0.000 | 0.000 | 0.000 | 0.000 | 0.070 | 0.000 | 0.000 | 0.113 | 0.429 | 0.932 |
| DARC | rs2814778 | C | 1.000 | 1.000 | 1.000 | 0.995 | 0.800 | 1.000 | 1.000 | 0.738 | 0.000 | 0.000 |
| DARC | rs3027011 | G | 0.080 | 0.123 | 0.081 | 0.102 | 0.185 | 0.121 | 0.185 | 0.058 | 0.000 | 0.000 |
| DARC | rs55872368 | T | 0.925 | 0.882 | 0.929 | 0.898 | 0.730 | 0.879 | 0.825 | 0.700 | 0.131 | 0.000 |
| DARC | rs7550207 | C | 0.080 | 0.123 | 0.081 | 0.097 | 0.190 | 0.121 | 0.185 | 0.125 | 0.197 | 0.000 |
| DARC | rs863004 | T | 0.925 | 0.882 | 0.929 | 0.903 | 0.760 | 0.874 | 0.825 | 0.771 | 0.404 | 0.034 |
| G6PD | rs1050828 | T | 0.040 | 0.070 | 0.160 | 0.210 | NA | 0.180 | NA | NA | 0.000 | 0.000 |
| G6PD | rs1050829 | C | 0.360 | 0.280 | 0.350 | 0.380 | NA | 0.340 | NA | NA | 0.000 | 0.000 |
| HBB (HbS) | rs334 | A | 0.115 | 0.123 | 0.121 | 0.139 | 0.005 | 0.101 | 0.070 | 0.000 | 0.000 | 0.000 |
| HBB (HbC) | rs33930165 | T | 0.004 | 0.006 | 0.000 | 0.028 | 0.005 | 0.000 | 0.020 | 0.000 | 0.000 | 0.000 |
| Skin pigmentation | ||||||||||||
| DDB1 | rs11230664 | T | 0.208 | 0.229 | 0.455 | 0.310 | 0.195 | 0.253 | 0.255 | 0.296 | 0.995 | 0.971 |
| HERC2 | rs4932620 | T | 0.071 | 0.076 | 0.096 | 0.083 | 0.030 | 0.131 | 0.100 | 0.242 | 0.010 | 0.019 |
| HERC2 | rs6497271 | G | 0.549 | 0.559 | 0.722 | 0.699 | 0.475 | 0.712 | 0.410 | 0.467 | 0.015 | 0.029 |
| KITLG | rs12821256 | C | 0.000 | 0.000 | 0.000 | 0.000 | 0.005 | 0.000 | 0.000 | 0.004 | 0.131 | 0.000 |
| MFSD12 | rs10424065 | T | 0.389 | 0.394 | 0.273 | 0.269 | 0.130 | 0.253 | 0.235 | 0.304 | 0.005 | 0.000 |
| MFSD12 | rs6510760 | A | 0.907 | 0.853 | 0.849 | 0.898 | 0.675 | 0.818 | 0.815 | 0.529 | 0.051 | 0.078 |
| OCA2 | rs1800404 | T | 0.150 | 0.082 | 0.136 | 0.069 | 0.145 | 0.086 | 0.045 | 0.258 | 0.823 | 0.393 |
| OCA2 | rs1800417 | G | 0.027 | 0.059 | 0.086 | 0.042 | 0.160 | 0.076 | 0.040 | 0.013 | 0.000 | 0.000 |
| SLC24A5 | rs1426654 | A | 0.075 | 0.088 | 0.025 | 0.014 | 0.075 | 0.076 | 0.025 | 0.371 | 1.000 | 0.029 |
| SLC45A2 | rs16891982 | G | 0.004 | 0.012 | 0.000 | 0.000 | 0.000 | 0.005 | 0.005 | 0.021 | 0.980 | 0.015 |
| TMEM138 | rs7948623 | T | 0.270 | 0.241 | 0.177 | 0.264 | 0.230 | 0.348 | 0.295 | 0.425 | 0.000 | 0.000 |
| TYR | rs1042602 | A | 0.000 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.013 | 0.399 | 0.000 |
| Trypanosomiasis | ||||||||||||
| APOL1 | rs60910145 | G | 0.243 | 0.123 | 0.495 | 0.375 | 0.120 | 0.056 | 0.055 | 0.000 | 0.000 | 0.000 |
| APOL1 | rs73885319 | G | 0.243 | 0.123 | 0.495 | 0.375 | 0.125 | 0.056 | 0.055 | 0.000 | 0.000 | 0.000 |
| APOL1 | rs143830837 | – | 0.195 | 0.182 | 0.116 | 0.079 | NA | 0.091 | NA | NA | 0.000 | 0.000 |
DA, derived allele; NA, missing data; Frequency of 0.000, not observed in that population.
Population codes: Esan in Nigeria (ESN); Yoruba in Ibadan, Nigeria (YRI); Gambian in Western Divisions in the Gambia (GWD); Mende in Sierra Leone (MSL); Luhya in Webuye, Kenya (LWK); Han Chinese in Beijing, China (CHB), Utah Residents with Northern and Western European Ancestry (CEU) from KGP Phase 3 and Baganda (BAG), Zulu (ZUL), Ethiopian (ETH) populations from AGVP. Both KGP Phase 3 and AGVP dataset have ∼100 individuals per population.