Thousands of risk variants underlying complex phenotypes (quantitative traits and diseases) have been identified in genome-wide association studies (GWAS). However, there are still two major challenges towards deepening our understanding of the genetic architectures of complex phenotypes. First, the majority of GWAS hits are in non-coding region and their biological interpretation is still unclear. Second, accumulating evidence from GWAS suggests the polygenicity of complex traits, i.e. a complex trait is often affected by many variants with small or moderate effects, whereas a large proportion of risk variants with small effects remain unknown.