Table 1 Association of established type 1 diabetes (T1D) loci with latent autoimmune diabetes in adulthood (LADA). Only T1D variants significantly associated with LADA are shown (LADA association P value), as well as signals significantly different between LADA and T1D (LADA vs. T1D P value), with a significance threshold of P = 7.46 × 10^–4. The locus reported is the closest gene of interest to the signal (a full list of genes is provided in Additional file 1: Table S2). The risk and other alleles reported refer to the alleles in T1D, and the following allele frequencies refer to the frequency of the risk allele reported in T1D for LADA, T1D, and Bone Mineral Density in Childhood Study (BMDCS) control group. Odds ratios of the risk allele reported are derived from the BMDCS control data set (n = 1057), the Wellcome Trust Case Control Consortium T1D (n = 1990), and the LADA cases (n = 978)

MHC

rs9272346

A/G

1.455 (1.427–1.483)

9.6 × 10^–11

1.26 × 10^–17

PTPN22

rs6679677

A/C

1.469 (1.427–1.510)

6.38 × 10^–6

2.61 × 10^–2

SH2B3

rs17696736

G/A

1.277 (1.250–1.304)

1.10 × 10^–5

0.542

INS

rs689

T/A

1.265 (1.234–1.296)

2.39 × 10^–4

3.88 × 10^–4

SMARCE1

rs7221109

C/T

0.954 (0.925–0.983)

0.423

6.54 × 10^–4