Table 1.

Allelic frequencies and association for the Gambian case-control study

SNPs	RS	Function	Alleles*	Minor allele freq.		HWE **	Allelic-based tests ***				Genotype-based tests ****
	number			Controls (628)	Cases (1534)	P-value	OR	95% CI		P-value	genotypes	OR	95% CI		P-value
HbS	rs334	C,Sy	A,S	0.080	0.012	0.54	0.14	0.10	0.21	<0.0001	AS v AA	0.07	0.04	0.12	<0.0001
MICB(i)	rs2534685	NA	A,G	0.471	0.496	<0.0001	1.10	0.96	1.26	0.15	AG v AA/GG	1.42	1.09	1.86	0.01
MICB(ii)	rs2516412	NA	C,A	0.450	0.436	<0.0001	0.94	0.82	1.08	0.41	AC v AA/CC	1.07	0.87	1.33	0.51
BAT1(i)	rs1129640	C,Sy	G,A	0.283	0.291	0.14	1.04	0.89	1.22	0.61	AG v AA/GG	1.18	0.94	1.48	0.15
rs928815	rs928815	NA	C,A	0.417	0.419	0.68	1.01	0.88	1.15	0.89	AA/AC v CC	0.97	0.78	1.20	0.78
LTA+80	rs2239704	UTR	G,T	0.419	0.416	0.77	0.99	0.86	1.13	0.80	GG/GT v TT	0.82	0.65	1.04	0.11
TNF-1031	rs1799964	P	T,C	0.128	0.137	0.15	1.08	0.89	1.32	0.42	CT v CC/TT	1.24	0.97	1.58	0.09
TNF-308	rs1800629	P	G,A	0.150	0.167	0.52	1.14	0.95	1.36	0.17	AA/AG v GG	1.12	0.91	1.41	0.28
TNF-238	rs361525	P	G,A	0.058	0.075	0.03	1.33	1.01	1.75	0.04	AG v GG/AA	1.58	1.15	2.17	0.005
AIF1(i)	rs2259571	I,NS	A,C	0.038	0.022	0.02	0.57	0.39	0.84	0.004	CC/AC v AA	0.61	0.40	0.93	0.02
AIF1(ii)	rs2269475	C,NS	G,A	0.181	0.205	0.38	1.17	0.98	1.38	0.08	AA/AG v GG	1.12	0.91	1.39	0.28
BAT2(i)	rs1046089	C,NS	A,G	0.475	0.398	0.15	0.73	0.64	0.84	<0.0001	GG v AA/AG	0.48	0.37	0.64	<0.0001

OR = odds ratios, CI = confidence interval, NA = not known, C = coding, I = intron, NS = non-synonymous, Sy = synonymous, P = promoter, () = sample size

^*alleles = major, minor alleles

^**one degree of freedom chi-square test of Hardy-Weinberg equilibrium applied to the 628 controls

^***adjusted for ethnicity and HbS

^****we performed additive, dominant, recessive and heterozygous advantage genotypic tests, adjusted for ethnicity and HbS, but only the most statistically significant result is presented; in bold P≤0.004