Table 4.

Association between established type 2 diabetes (T2D) loci in latent autoimmune diabetes in adulthood (LADA) cases positive for glutamic acid decarboxylase autoantibodies (GADA) and insulinoma-associated antigen-2 autoantibodies (IA2A). T2D variants that were significantly associated in LADA cases positive for GAD and IA2 autoantibodies (n = 309) (LADA association P value) are shown, as well as signals that were significantly different between LADA and T2D cases (LADA vs. T2D P value). The significance threshold was set to P < 7.04 × 10^–4 to correct for multiple testing. The locus reported is the closest, well-known gene of interest to the signal (a full list of genes is provided in Additional file 1: Table S5). T2D risk allele frequencies reported are derived from the Bone Mineral Density in Childhood Study control data set (n = 1057), the Wellcome Trust Case Control Consortium T2D (n = 1960), and the LADA cases positive for autoantibodies GADA and IA2A (n = 309). The odds ratios for LADA are shown both GEMMA-corrected (for relatedness and batch effects) and uncorrected

Locus	SNP	T2D alleles risk/other	Risk allele frequency			LADA odds ratio	LADA P value	LADA vs. T2D P value
			LADA	T2D	Control
HNF1A	rs12427353	G/C	0.857	0.828	0.787	1.474 (1.438–1.511)	2.52 × 10–4	5.42 × 10–2
ZBED3	rs6878122	A/G	0.744	0.658	0.706	1.216 (1.184–1.249)	3.86 × 10–2	1.47 × 10–5
TCF7L2	rs7903146	T/C	0.251	0.376	0.298	0.852 (0.820–0.883)	8.14 × 10–2	2.56 × 10–7