The GIANT Consortium performed a meta-analysis of GWAS data in a discovery set with 133,653 and 123,865 individuals of recent European ancestry from 46 studies for height3 and BMI4, respectively. In each of the participating studies, genotype data were imputed to ~2.8 million SNPs present in the HapMap Phase 2 European-American reference panel26, and the standard errors of all SNPs were adjusted by the genomic control method20. We calculated the effective sample size for each SNP and excluded SNPs with effective sample sizes of >2 s.d. from the mean. We also excluded SNPs with MAF of <0.01, retaining ~2.5 million SNPs for both height and BMI.
