The results reported here are all based on GWAS of European cohorts, thus we used the European panel from 1KG as reference panel. To evaluate whether this panel approximates LD matrices derived from other European cohorts sufficiently well, we compared results when using genotypes taken from the CoLaus cohort as reference panel[27]. We saw good concordance between the different reference panels for both the sum and the max gene scores for the largest HDL blood lipid GWAS to-date[23] (S2 Fig).
