For each of the previously known loci except ABCA1 (9q31), at least one of the candidate associations was nominally significant ( P <0.05, two-sided) in at least one of the replication cohorts or in analysis combining p-values from the two replication cohorts when effect estimates (beta coefficients) indicated trends in lipoprotein measure consistent with the effects observed in the WGHS.
Consistent with a high degree of correlation among the lipoprotein measures ( Table S2 ), the rank order by p-value among the highly significant SNPs was similar for each measure with at least one genome-wide significant association ( Figure S1 ).
Nevertheless, ongoing genotyping in the WGHS of an additional 4639 samples (3305 with fasting status) completed subsequent to the main analysis provided significant support for these last two loci on the basis of internal replication, as well as significant or borderline significant support for four others, confirming directions of effects for all novel candidate associations, and leading to smaller p-values in analysis combining the main WGHS sample with the additional samples for all but three entries in Table 3 and at least one lipoprotein measure for each locus (compare to Table S1 ).