Annotation of eQTLS with Respect to RNA Regulatory Sites (2014)

Undergraduate: Charles Czysz

Faculty Advisor: Alain Laederach
Department: Biology

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Many variations in phenotype between individuals are the result of single nucleotide polymorphisms(SNPs). If a SNP occurs in a regulatory region, it can lead to changes in gene expression levels. Such SNPs which affect mRNA levels are called expression quantitative trait loci. I sought to find eQTLs whose mechanism of action directly affects RNA, as opposed to pre-transcriptional regulation, specifically by altering the binding of small interfering RNA or RNA-binding proteins. Changes in these processes can be due to RNA conformational change or changes in recognition sites, and are important in finding causes of RNA diseases. I computationally analyzed overlap of eQTLs with regulatory sites using SNP data from HapMap and 1000Genomes, eQTL data from the NIH GTEx Project, and regulatory sites from the ENCODE project and other public databases. My goal is to find eQTLs whose mechanism of action directly affects RNA.