The T1DGC linkage scan shows significant linkage to the HLA region on chromosome 6p21 (LOD = 213.2), and suggestive linkage (2.2<LOD<3.6) to regions on chromosomes 2q32, 11p15, 19p13 and 19q12. Because the well-known underlying genetic effects in the HLA region (OR = 5.5) and 11p15 (INS, OR = 2.4) are among the strongest documented in complex disease, the linkage results at these two loci are unsurprising. The linkage signal on 2q32 could in theory be driven by synthetic associations directly under the peak (CTLA4 (OR = 1.2) and STAT4 (OR = 1.1) [20]), but could also be amplified by three other associations also on 2q. No documented associations (synthetic or otherwise) lie under either peak on chromosome 19. To investigate the possibility that some GWAS loci may be contained within regions displaying weak evidence of linkage (LOD>1.5), we extended the search to include an extra four such loci but did not identify any further overlaps. The remaining 47 type 1 diabetes risk loci [20] therefore show no evidence of linkage. Indeed, for complex diseases more generally there has been little
