Computational protocol: Investigation of single and synergic effects of NLRC5 and PD-L1 variants on the risk of colorectal cancer

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Protocol publication

[…] SNPs were selected using several in silico tools, such as UCSC browser ( to collect all potential functional SNPs in the regulatory regions, HaploReg ( and Regulome DB ( to explore the chromatin state, conservation, and regulatory motif alterations within sets of genetically linked variants, Gtex Portal ( to identify all cis-eQTL SNPs that affect the expression of genes of our interest and microRNA binding site prediction tools (, to investigate the 3’-UTR and to predict if a SNP within the target site will disrupt/eliminate or enhance/create a microRNA binding site. PERFECTOS-APE ( and s-Transcription factor Affinity Prediction (s-TRAP, were used to identify transcription factors whose binding sites can be significantly affected by a given polymorphism. LD and the haplotype blocks within the genes were examined based on r2 (). […]

Pipeline specifications

Software tools HaploReg, MicroSNiPer, PERFECTOS-APE, TRAP
Databases RegulomeDB
Application sRNA-seq analysis
Organisms Homo sapiens
Diseases Neoplasms, Colorectal Neoplasms