With the functional annotation data from RegulomeDB, in the ASB16-AS1 locus we found that rs184478, which was in perfect LD with rs227580 (Fig. 3), was an eQTL overlapping with many functional regions such as conserved motifs, transcription factor binding site, DNase I hypersensitive peak, Chip-Seq peaks and DNase I footprint region, while the top cis-eQTL rs227580 only overlapped with transcription factor binding site and DNase I hypersensitive peak. The PICS score of rs184478 was 0.987, while the PICS score of rs2275580 was only 0.055. When using rs184478 instead to perform the SMR test, we found the Psmr value (Psmr = 2.39 × 10−8) was smaller (thus more significant) than using the top cis-eQTL (Psmr = 1.30 × 10−7). In the SYN2 locus, rs795000 achieved the highest PICS score. When using rs795000 instead to perform the SMR test, the result was more significant than using the top cis-eQTL rs310758 (Table 1). Therefore, rs184478 and rs795000 had the largest possibility to be causal SNPs for ASB16-AS1 and SYN2 genes, respectively.
