Table 4 Primary statistical analysis of type 1 diabetes.

Chr	SNP	Gene of interest	Minor allele	MAF	HR (95% CI) Subjects with T1D (n = 115) vs subjects without T1D (n = 5359)	p
1	rs665691	C1qC	G	0.44829	1.10 (0.86–1.41)	0.4540
1	rs17615	CD21	A	0.29459	1.24 (0.94–1.65)	0.1296
1	rs1048971	CD21	A	0.34597	1.14 (0.87–1.50)	0.3333
1	rs4308977	CD21	C	0.29010	1.23 (0.93–1.62)	0.1499
1	rs4844573	C4BPA	C	0.37678	0.82 (0.62–1.08)	0.1635
6	rs9332739	C2	C	0.06065	1.08 (0.64–1.80)	0.7848
6	rs2857009	C4	C	0.40608	1.02 (0.73–1.44)	0.8984
9	rs10818488	C5	A	0.45661	1.15 (0.90–1.46)	0.2693
9	rs7029078	C5	G	0.37450	1.12 (0.86–1.47)	0.3954
16	rs1143678	ITGAM	T	0.14770	0.84 (0.59–1.20)	0.3447
16	rs1143683	ITGAM	T	0.14773	0.84 (0.58–1.20)	0.3363
16	rs1143679	ITGAM	A	0.11538	0.66 (0.43–1.04)	0.0709
16	rs4597342	ITGAM	T	0.33638	1.05 (0.81–1.37)	0.6935
19	rs2230199	C3	C	0.19865	1.30 (0.95–1.79)	0.1019
19	rs7951	C3	A	0.08916	0.90 (0.56–1.44)	0.6591

A total of 15 SNPs on the ImmunoChip were interrogated in The Environmental Determinants of Diabetes in the Young (TEDDY) study in 115 subjects that had developed type 1 diabetes versus all other subjects (n = 5359). Subjects eligible for TEDDY carried any of the high risk HLA-DR-DQ genotypes. The minor allele frequency (MAF) was calculated from all subjects (n = 5474). Proportional hazard models were adjusted for HLA genotypes, sex and country of residence and population stratification. The first two principal components resulting from a principal components analysis of the US participants were included in the model to adjust for population stratification. First degree relatives were excluded from the analyses. Hazard ratios (HR) and 95% confidence intervals (95% CI) were estimated in this time-to-event analysis. A robust variance estimate was used to account for the dependence within families in the models. For a Chi-square value to remain significant after Bonferroni correction for multiple comparisons of 15 SNPs it must be less than 0.00333.
Abbreviations:
CD21: C3D-receptor, complement receptor type 2, EBV-receptor, ITGAM: Integrin alpha M = MAC1 or complement receptor 3, C4BPA: C4 binding protein alpha chain.

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