To identify putative causal variants among the height-associated markers, we explored whether the height-associated SNPs were in strong LD (r2>0.8) with non-synonymous coding variants in 1000 Genomes Project CEU Phase 1 data, showed an effect on whole blood gene expression levels, were located within ENCODE-annotated regions, were within loci harboring monogenic growth genes, or had previously been associated with other complex traits in NHGRI GWAS catalog (P<5×10−8) (Supplementary Tables 7–11). To estimate the empirical assessment of enrichment for listed features we used 10,000 permutations of random sets of SNPs matched to the pruned (LD r2>0.1) 628 height-associated SNPs by the number of nearby genes (within a distance of LD r2>0.5), physical distance to nearest gene, and minor allele frequency.
