of 718 SNPs in the 1000 genomes reference panel, of which we were able to on average accurately impute 261 (see Table S9). This resulted in 2837 (10778), 1231 (3903), 1693 (5504), 1615 (5513) SNPs (with 1 KG imputation) to which we fit our model for HDL, LDL, TC, and TG respectively. In addition, we created the corresponding pool of functional annotations described above for every SNP in a window. We analyzed the dataset using PAINTOR in two phases. In the first phase we fit our model for each annotation independently to ascertain the functional annotations most phenotypically relevant. We did this for all four lipid traits for both the original and densely imputed data sets. After running PAINTOR marginally on each annotation, we selected the the top five most significant annotations for the final model (denoted with a * in Table: 5). We note that in the case of experimental replicates (i.e. same tissue and class), we only report the top replicate.
