Table 1 and Tables S1 through S3 display the results of the test of association between case-control status in the WTCCC and weighted genome-wide allelic scores calculated from all SNPs across the genome (i.e. the columns in Table 1 labelled “GW Score”), a weighted allelic score constructed from variants in known regions which met p<5×10−8 in the relevant GWAS meta-analysis (i.e. the columns in Table 1 labelled “Known”), and a weighted genome-wide score with SNPs from known regions removed from its construction (i.e. the columns in Table 1 labelled “Complement”). In the case of BMI, an allelic score consisting of known variants only showed strong evidence of being related to type 2 diabetes in the expected direction. As the threshold for SNP inclusion became more relaxed, the BMI score also showed nominal evidence of association with other diseases most notably bipolar disorder. These genome-wide scores were also very strongly related to risk of type 2 diabetes, more so than the score constructed from the known regions only. This is expected if the relationship between BMI and type 2 diabetes is
