Table 1. SNP markers and association in follow-up study.

			(A) Dutch (446 cases, 641 controls)				(B) Finnish (623 cases, 359 healthy)			(C) Hungarian (592 cases, 471 healthy)			(D) Finnish, Hungarian, Dutch (1661 cases, 1471 controls)
Markers	Position (bp)	Alleles	Case, contr freq	P value	emp P-value	OR (95% CI)	Case, contr freq	P value	OR (95% CI)	Case, contr freq	P value	OR (95% CI)	Case, contr freq	P value	OR (95% CI)
rs1648957	104613397	CT	0.498, 0.433	0.003	0.005	1.30 (1.09–1.55)	0.449, 0.481	0.351		0.545, 0.519	0.440		0.498, 0.460	0.085
rs9391227	105265327	AT	0.497, 0.559	0.005	0.003	0.78 (0.66–0.93)	0.541, 0.651	0.003*	0.66 (0.49–0.88)	0.495, 0.555	0.054		0.507, 0.577	3.07 × 10−5*	0.76 (0.66–0.86)
rs2895615	106292441	CG	0.690, 0.642	0.020	0.018	1.25 (1.03–1.50)	0.668, 0.641	0.398		0.679, 0.678	0.871		0.683, 0.649	0.061
rs2216084	107660005	CT	0.646, 0.688	0.045	0.058	0.83 (0.69–0.99)	0.809, 0.757	0.048	1.41 (0.99–1.99)	0.706, 0.676	0.603		0.700, 0.699	0.836
rs1146229	109205720	CT	0.085, 0.052	0.002	0.003	1.72 (1.22–2.43)	0.111, 0.118	0.673		0.070, 0.095	0.082		0.087, 0.075	0.259
rs9487060	109741149	CG	0.079, 0.048	0.003	0.002	1.73 (1.21–2.47)	0.067, 0.072	0.724		0.060, 0.062	0.763		0.072, 0.054	0.032	1.36 (1.03–1.79)
rs2503770	110373108	AT	0.233, 0.274	0.031	0.028	0.80 (0.66–0.98)	0.324, 0.313	0.884		0.237, 0.217	0.376		0.255, 0.269	0.536
rs571060	112403213	CT	0.970, 0.987	0.007	0.010	0.44 (0.24–0.81)	0.992, 0.993	1.000		0.982, 0.978	0.841		0.978, 0.986	0.085
rs2282854	112638353	CT	0.933, 0.962	0.003	0.003	0.55 (0.37–0.82)	0.968, 0.965	0.796		0.948, 0.938	0.452		0.946, 0.958	0.170
rs4946111	116091112	GT	0.445, 0.502	0.011	0.008	0.80 (0.67–0.95)	0.385, 0.482	0.007	0.66 (0.49–0.90)	0.434, 0.390	0.280		0.429, 0.474	0.020	0.86 (0.76–0.98)
rs1998166	117020110	CT	0.921, 0.877	0.001	0.003	1.62 (1.20–2.19)	0.940, 0.917	0.105		0.956, 0.928	0.087		0.934, 0.896	2.17 × 10−4*	1.56 (1.22–1.98)
rs4946578	121936760	AG	0.584, 0.534	0.023	0.023	1.23 (1.03–1.46)	0.732, 0.695	0.323		0.564, 0.536	0.421		0.606, 0.558	0.002	1.25 (1.09–1.44)

Abbreviations: contr, control; freq, frequency.

SNP markers in the study and their association to celiac disease in Dutch cases and controls (A) as well as Finnish (B) and Hungarian (C) families, and a meta-analysis of all three populations (D). Case frequencies, in the family materials, refer to the allele frequencies of the affected offspring (‘cases') and the control frequencies refer to both unaffected offspring (‘healthy') and the untransmitted alleles in parents. P-values lower than 0.01 are considered significant (marked in bold) and odds ratios (OR) and 95% confidence intervals for significant markers are given.

Emp permutation P-values are based on 10 000 permutations.