It was reported that many active chromatin marks are located in the intronic and exonic region of genes (47). Enhancers can also reside in intronic region of a gene to coordinate the looping with active promoter of another gene (48). Even for validated human fragments with enhancer activity (49), we found 30.42% of these fragments overlapped with coding region of genes. Thus, genetic variants not belonging to non-coding RNAs may also be associated with gene regulation. On the other hand, an exonic variant can associate with particular regulatory process by linking variants in the LD proxy. GWAS3D not only provides an efficient solution to interpret the regulatory role of genetic variation in the noncoding regions but also in other genic regions.
