Empowered by advances in sequencing technologies, attention is currently shifting towards the comprehensive study of low-frequency and rare variants. Resources such as the 1000 genomes project and emerging large-scale studies like the UK10k project will undoubtedly facilitate the examination of variants at this end of the allele frequency spectrum. In parallel, improved strategies for accurate imputation and powerful analysis of low-frequency and rare variants in aggregate are being further developed and fine-tuned to the needs of these next generation truly genome-wide scans for association.