Table 3

Allele frequencies (F1) and p-values of single-locus association in the three studies

	dbSNP ID	Frequency (F1%)		Association (p)		Odds ratio (MA)
	dbSNP ID	Cases	Controls	Allelic	Genotypic	OR	95% CI
Significant single locus association of htSNPs are indicated in bold. Odds ratios and their 95% confidence interval are presented for the minor allele versus the major allele for all htSNPs. The p values were derived by standard Pearson’s χ² tests except in cases where cell counts in the contingency tables were less than 5. When cell counts were less than 5 (*), p values were determined empirically by 100 000 simulations (CLUMP software).
†A genotypic test was not carried out for the del-In9 in intron 9 in the CBD series, as there were no rare homozygotes in the CBD cases, thus preventing us from performing a valid test.
CI, confidence interval; MA, minor allele; OR, odds ratio.
US PSP
8	rs1467967	62.8	62.6	0.963	1.000	0.965	0.703 to 1.325
14	rs242557	54.4	31.0	2.91ex⁻⁹	2.29ex⁻⁸	2.356	1.706 to 3.255
17	rs3785883	17.0	22.4	0.072	*0.168	0.713	0.487 to 1.044
21	rs2471738	67.0	81.5	1.87ex⁻⁵	*1.15ex⁻⁴	2.224	1.535 to 3.222
del-In9	….	91.6	77.1	4.02ex⁻⁸	*1.00ex⁻⁵	0.298	0.193 to 0.462
25	rs7521	43.2	44.5	0.456	0.671	1.124	0.827 to 1.526

UK PSP
8	rs1467967	67.9	64.6	0.993	0.770	0.998	0.639 to 1.560
14	rs242557	47.9	35.7	0.012	0.016	1.815	1.209 to 2.726
17	rs3785883	25.5	20.6	0.365	0.680	1.227	0.762 to 1.974
21	rs2471738	66.0	80.1	0.001	0.005	2.142	1.368 to 3.355
del-In9	….	93.2	76.6	1.14ex⁻⁵	5.31ex⁻⁵	0.215	0.099 to 0.466
25	rs7521	51.2	45.7	0.546	0.814	0.773	0.505 to 1.183

US CBD
8	rs1467967	61.9	62.6	0.909	*0.870	1.030	0.619 to 1.713
14	rs242557	50.0	31.0	0.002	0.010	2.231	1.322 to 3.764
17	rs3785883	33.3	22.4	0.019	0.022	1.047	0.586 to 1.872
21	rs2471738	67.0	81.5	0.005	0.011	2.165	1.254 to 3.736
del-In9	….	86.4	77.1	0.063	†	0.532	0.271 to 1.043
25	rs7521	43.2	44.5	0.826	0.464	0.807	0.494 to 1.320