result of random sampling. We show with empirical data that the observed LD correlation between SNPs more than 10 Mb apart is consistent with what we would expect by chance (Supplementary Fig. 7). We use the expected values (zeros) in the matrix B for such pairs of distant SNPs, because it is more appropriate to represent a sampled correlation observed in the meta-analysis sample by its expected value rather than another sampled correlation observed in the reference sample unless the whole meta-analysis sample is used as the reference sample.
