Strong cis-acting expression quantitative trait loci for the genes encoding SNHG5 and PEX6

Abstract

Expression of quantitative trait loci (eQTLs) for the genes located in human chromosome 6 were examined. Data on RNA expression in lymphoblastoid cells of 373 unrelated Europeans were used to identify eQTLs. Genome-wide analysis resulted in 24,447 nucleotide variants associated with gene expression (P < 2.16 x 10(-10)). We found 36variants with P < 10(-100), which were all associated with expression levels of the genes encoding small nucleolar RNA host gene 5 (SNHG5) and peroxisomal biogenesis factor 6 (PEX6). Enhancer eQTLs downstream of the SNHG5 gene might be candidate genetic factors for susceptibility to cancer. This is because nucleotide substitutions (eg, G -> T at rs6922) of the enhancer eQTLs may cause low expression of SNHG5 gene, and low expression of snoRNA U50, a product generated from introns of the SNHG5gene, can induce cancer. One presently identified eQTL for the PEX6 gene was rs10948059, which had been associated with prostate cancer from previous association studies. The results imply that variants associated with prostate cancer can be identified through expressional change in the PEX6 gene, but not in the overlapped glycine N-methyltransferase gene which had been considered as a candidate gene. Further studies are required to understand their underlying mechanisms for the strong eQTLs for the SNHG5 and PEX6 genes.