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Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression

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posted on 17.01.2013, 01:14 by Vinod Kumar, Harm-Jan Westra, Juha Karjalainen, Daria V. Zhernakova, Tõnu Esko, Barbara Hrdlickova, Rodrigo Almeida, Alexandra Zhernakova, Eva Reinmaa, Urmo Võsa, Marten H. Hofker, Rudolf S. N. Fehrmann, Jingyuan Fu, Sebo Withoff, Andres Metspalu, Lude Franke, Cisca Wijmenga

Recently it has become clear that only a small percentage (7%) of disease-associated single nucleotide polymorphisms (SNPs) are located in protein-coding regions, while the remaining 93% are located in gene regulatory regions or in intergenic regions. Thus, the understanding of how genetic variations control the expression of non-coding RNAs (in a tissue-dependent manner) has far-reaching implications. We tested the association of SNPs with expression levels (eQTLs) of large intergenic non-coding RNAs (lincRNAs), using genome-wide gene expression and genotype data from five different tissues. We identified 112 cis-regulated lincRNAs, of which 45% could be replicated in an independent dataset. We observed that 75% of the SNPs affecting lincRNA expression (lincRNA cis-eQTLs) were specific to lincRNA alone and did not affect the expression of neighboring protein-coding genes. We show that this specific genotype-lincRNA expression correlation is tissue-dependent and that many of these lincRNA cis-eQTL SNPs are also associated with complex traits and diseases.

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