An increasing number of studies also suggest that functionally annotated SNPs are generally more biologically important than those that are not annotated, and henceforth more likely to be associated with complex traits. To name a few, using GWAS data of different traits (e.g., Crohn's disease and SCZ), Schork et al. [20] demonstrated a consistent pattern of enrichment of GWAS signals among functionally annotated SNPs. Yang et al. [21] showed that SNPs in genic regions could explain more variance of height and body mass index (BMI) than SNPs in intergenic regions. Nicolae et al. [22] found that SNPs associated with complex traits were more likely to be expression quantitative trait loci (eQTL). In addition, public availability of a vast amount of functional annotation data also provides unprecedented opportunities to investigate the enrichment of GWAS signals among these various types of functional annotations. For example, the Encyclopedia of DNA Elements (ENCODE) Consortium has recently generated extensive experimental data on gene expression (RNA-seq), DNA methylation status (RRBS-seq), chromatin modifications (ChIP-seq), chromatin accessibility (DNase-seq and FAIRE-seq), transcription factor (TF) binding sites (ChIP-seq), and long-range
