For most complex diseases, the fraction of heritability that can be explained by the variants discovered from genome-wide association studies is minor. Although the so-called “rare variants” have attracted increasing attention, they are unlikely to account for much of the “missing heritability,” since few people carry them. The genetic variants that are likely to fill in the “missing heritability” include uncommon causal variants, which are generally untyped in association studies using tagging single-nucleotide polymorphisms (SNPs) or commercial SNP arrays. Developing powerful statistical methods can help identify chromosomal regions harboring uncommon causal variants, while bypassing the genome-wide or exome-wide next-generation sequencing.