SUGEN association results were used for the identification of novel and secondary findings for all phenotypes. The variant with the smallest P value in a 1-Mb region was considered the ‘lead SNP. A lead SNP was considered to be a novel locus if it met the following criteria: (1) the lead SNP was located greater than ±500 kb away from a previously known locus (per the phenotype-specific list of known loci); (2) had a SUGEN P < 5 × 10−8; (3) had a SUGEN conditional P < 5 × 10−8 after adjustment for all previously known loci on the same chromosome; and (4) had two or more neighbouring SNPs (within ±500 kb) with a P < 1 × 10−5. A lead SNP was considered to be a secondary signal in a previously known loci if it met the following criteria: (1) the lead SNP was located within ±500 kb of a previously known loci; (2) had a SUGEN P < 5 × 10−8; and (3) had a SUGEN conditional P < 5 × 10−8 after adjustment for all previously known loci on the same chromosome. Full results for all novel and secondary findings are included in Supplementary Tables 2, 3.
