Table 3.

Association of established type 2 diabetes (T2D) loci with latent autoimmune diabetes in adulthood (LADA). Only T2D variants significantly associated with LADA after correcting for multiple comparison (P < 7.04 × 10^–4) are shown (LADA association P value), as well as variants significantly different between LADA and T2D (LADA vs. T2D P value). The locus reported is the closest, well-known gene of interest to the signal (a full list of genes are provided in Additional file 1: Table S4). The risk and other alleles reported refer to the alleles in T2D, and the following allele frequencies refer to the frequency of the risk allele reported in T2D, for LADA, T2D, and Bone Mineral Density in Childhood Study (BMDCS) control groups. Odds ratios of the risk allele reported are derived from the BMDCS control data set (n = 1057), the Wellcome Trust Case Control Consortium T2D (n = 1960), and the LADA cases (n = 978)

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	0.831	0.828	0.787	1.291 (1.256–1.326)	3.42 × 10–4	0.538
TCF7L2 a	rs7903146	T/C	0.295	0.376	0.298	1.023 (0.994–1.053)	0.702	5.21 × 10–6

^aAlthough the control risk allele frequency is greater than the case risk allele frequency, the beta calculated from the linear mixed model is adjusted effects after controlling for population stratification, resulting in an OR slightly above 1