Table 3 Primary statistical analysis of islet autoimmunity (IA).

Chr	SNP	Gene of interest	Minor allele	MAF	HR (95% CI) IA positive subjects (n = 413) vs subjects with no IA (n = 5061)	p
1	rs665691	C1qC	G	0.44829	0.98 (0.85–1.12)	0.7450
1	rs17615	CD21	A	0.29459	1.02 (0.88–1.19)	0.7638
1	rs1048971	CD21	A	0.34597	1.02 (0.88–1.18)	0.8277
1	rs4308977	CD21	C	0.29010	1.02 (0.88–1.19)	0.7540
1	rs4844573	C4BPA	C	0.37678	0.93 (0.81–1.07)	0.3332
6	rs9332739	C2	C	0.06065	1.04 (0.79–1.38)	0.7733
6	rs2857009	C4	C	0.40608	0.98 (0.82–1.18)	0.8539
9	rs10818488	C5	A	0.45661	1.11 (0.98–1.27)	0.1129
9	rs7029078	C5	G	0.37450	1.03 (0.90–1.18)	0.6711
16	rs1143678	*ITGAM*	T	0.14770	0.80 (0.66–0.98)	0.0324
16	rs1143683	*ITGAM*	T	0.14773	0.80 (0.65–0.98)	0.0301
16	rs1143679	ITGAM	A	0.11538	0.82 (0.66–1.01)	0.0667
16	rs4597342	*ITGAM*	T	0.33638	1.16 (1.01–1.32)	0.0406
19	rs2230199	C3	C	0.19865	0.94 (0.79–1.12)	0.4870
19	rs7951	C3	A	0.08916	0.90 (0.70–1.15)	0.3918

A total of 15 SNPs on the ImmunoChip were interrogated in The Environmental Determinants of Diabetes in the Young (TEDDY) study in 413 subjects positive for any IA versus 5061 autoantibody negative subjects. 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. The factors indicating nominal significant risk or protection are indicated in bold. 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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