probability of observing a LD correlation greater than 0.1 or smaller than –0.1 (r2 > 0.01) is 3.4 × 10–16. In order to investigate possible false positives resulting from errors in LD estimation, we first performed the analysis using the ARIC cohort as a reference sample, and we then performed a joint analysis of the selected SNPs using the QIMR cohort as a reference sample (Supplementary Tables 2 and 3). We show that the LD correlations between adjacent pairs of the 247 height-associated SNPs are in very good agreement across the ARIC and QIMR cohorts (Supplementary Fig. 5). Therefore, our main results were unlikely to be driven by errors in estimating the LD structure in the reference sample. This is consistent with our technical replication of all secondary signals reported by the GIANT Consortium from conditional analysis using individual-level genotype and phenotype data3. We reported most results based on the ARIC cohort (for example, Table 1) because it has a larger sample size and is more genetically similar to the whole GIANT meta-analysis sample relative to the QIMR cohort, where ancestry is restricted to the British Isles14. We could also only consider results that were consistent using two independent cohorts
