Linkage disequilibrium (LD) differences between populations can potentially result in failure to replicate primary signals of trait association in independent genome-wide association studies (GWAS). However, such inter-population LD differences can be leveraged to narrow the search for common causal variants responsible for the association signals observed. The ability to assess and quantify LD variations among populations is thus expected to contribute to both replication and fine-mapping stages of GWAS.