PXR and CAR single nucleotide polymorphisms influence plasma efavirenz levels in South African HIV/AIDS patients

BMC Medical Genetics

Table 5 Comparison of the allele frequencies between the South Africans and other populations

SNP ID	Minor allele	South Africans this study (n=464)	YRI HapMap (n=226)	CEU HapMap (n=226)	HCB HapMap (n=86)	Bushman dbSNP (n=3)
NR1I2 rs3732356T>G	G	0.234	0.254	0.033**	N/A	0.000**
NR1I2 rs2472677C>T	T	0.351	0.356	0.636**	0.544*	N/A
NR1I2 rs6785049G>A	A	0.040	0.000**	0.673**	0.453**	N/A
NR1I3 rs2307424C>T	T	0.047	0.119**	0.336**	0.512**	N/A
NR1I3 rs3003596T>C	C	0.416	0.612**	0.407	0.535	0.500
NR1I3 rs2502815C>T	T	0.230	0.406**	0.248	0.442**	0.500**
		n=32 ^#	n=226	n=226	n=86
NR1I2 rs12721601T>C	C	0.016	0.008	N/A	N/A	N/A
NR1I2 rs59371185G>A	A	0.016	0.000	N/A	N/A	N/A
NR1I2 rs12721613C>T	T	0.064	0.183*	0.000*	0.000*	N/A
NR1I2 rs1464603C>T	T	0.016	N/A	0.292**	0.325**	0.000
NR1I2 rs1464602C>T	T	0.313	0.186*	0.717**	0.675**	0.667**
NR1I2 rs80320762G>A	A	0.048	0.144*	N/A	N/A	N/A
NR1I2 rs12721616C>T	T	0.219	0.042**	N/A	N/A	N/A
NR1I2 rs112813596G>A	A	0.016	N/A	N/A	N/A	0.000
NR1I3 rs35205211C>G	G	0.032	N/A	N/A	N/A	0.005
NR1I3 rs34161743C>T	T	0.016	N/A	N/A	N/A	0.005
NR1I2 36726T>C^#	C	0.078	N/A	N/A	N/A	N/A
NR1I2 36857G>A^#	A	0.016	N/A	N/A	N/A	N/A
NR1I2 36905C>T^#	T	0.031	N/A	N/A	N/A	N/A

N/A = not available; *allele frequencies statistically significantly different from the South Africans (P<0.05), **allele frequencies statistically significantly different from the South Africans (P<0.001), ^#Sequencing according to the NR1I2 gene sequence [GenBank: AF364606] with the allele change for NR1I2 36857G>A according to the reverse sequence.

ISSN: 1471-2350