Table 4.

All allele defining variants and SNPs displaying significant differences in allele frequencies between the Khoisan (n = 29), Mixed Ancestry (n = 65), and Xhosa (n = 65).

Position in gene	Allele	rs number	Khoisan-mixed ancestry		Khoisan-xhosa		Mixed ancestry-xhosa
GenBank: AF280107.1			P-Value	OR (95% CI)	P-Value	OR (95% CI)	P-Value	OR (95% CI)
−392 A>GG>A	CYP3A4*1B	rs2740574	0.000	0.257 (0.125–0.525)	0.592	0.818 (0.392–1.705)	0.000	3.189 (1.876–5.421)
−292 T>G		Novel	0.619	1.769 (0.187–16.713)	0.041	21.343 (1.129–403.534)	0.093	15.894 (0.628–402.140)
3847 A>G		Novel	0.713	2.094 (0.041–106.852)	0.094	0.087 (0.005–1.508)	0.029	0.042 (0.002–0.716)
14268 C>T	CYP3A4*23	rs57409622	0.137	10.138 (0.478–214.853)	0.206	4.778 (0.424–53.807)	0.566	0.391 (0.016–9.687)
14269 G>A	CYP3A4*15	rs4986907	0.713	2.094 (0.041–106.852)	0.430	0.302 (0.015–5.935)	0.202	0.144 (0.007–2.818)
15649 A>T	CYP3A4*24	rs113667357	0.059	3.519 (0.953–12.993)	0.053	3.635 (0.985–13.414)	0.964	1.033 (0.253–4.2220)
15753 T>G		rs2687116	0.000	0.264 (0.132–0.529)	0.783	1.108 (0.534–2.298)	0.000	4.191 (2.447–7.180)
17829 T>C		Novel	0.025	11.981 (1.367–105.025)	0.025	11.981 (1.367–105.025)	1.000	1.000 (0.062–16.163)
20230 G>A	CYP3A4*1G	rs2242480	0.000	0.142 (0.053–0.378)	0.540	1.439 (0.450–4.603)	0.000	10.167 (4.583–22.553)
21896 C>T	CYP3A4*12	rs12721629	0.707	2.128 (0.042–108.589)	0.437	0.307 (0.016–6.030)	0.202	0.144 (0.008–2.817)
23081 C>T		rs12721620	0.083	0.161 (0.021–1.268)	0.013	0.077 (0.010–0.583)	0.043	0.477 (0.232–0.978)
25721 A>G		rs3735451	0.001	0.300 (0.143–0.629)	0.076	2.140 (0.922–4.965)	0.000	7.133 (3.718–13.685)

Variants showing significant differences between the South African populations are indicated in shaded areas (P < 0.05).