The functional scores for candidate SNPs were calculated using an aggregation of RegulomeDB and HaploReg v4; each provided the regulatory scores for candidate SNPs, including the items of protein binding, chromatin changing, and eQTL (table S5). The genomic sequences of multiple species were obtained from the UCSC Genome Browser to conduct the conservation assessment. Haplotter displayed the results of a scan for positive selection in the human genome and detected recent positive selection with iHSs (33). The Genotype-Tissue Expression project is a comprehensive public resource that was used to study tissue-specific eQTL. FIMO (19) and CTCFBSDB (20) were applied to predict the change in CTCF motif and binding sites affected by the risk variant. The mfold tool (34) calculated the energy change in DNA folding affected by the risk variant. The mature sequences of the GCLET transcript were derived from the Ensembl genome and LNCipedia v5.0 databases (35). Three stringent methods, CPAT (36), iSeeRNA (37), and PhyloCSF (38), were used to evaluate the coding probability of candidate lncRNAs.

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