Large intergenic noncoding RNAs (lincRNAs) are still poorly functionally 
characterized. We analyzed the genetic and epigenetic regulation of human 
lincRNA expression in the GenCord collection by using three cell types from 195 
unrelated European individuals. We detected a considerable number of cis 
expression quantitative trait loci (cis-eQTLs) and demonstrated that the genetic 
regulation of lincRNA expression is independent of the regulation of neighboring 
protein-coding genes. lincRNAs have relatively more cis-eQTLs than do equally 
expressed protein-coding genes with the same exon number. lincRNA cis-eQTLs are 
located closer to transcription start sites (TSSs) and their effect sizes are 
higher than cis-eQTLs found for protein-coding genes, suggesting that lincRNA 
expression levels are less constrained than that of protein-coding genes. 
Additionally, lincRNA cis-eQTLs can influence the expression level of nearby 
protein-coding genes and thus could be considered as QTLs for enhancer activity. 
Enrichment of expressed lincRNA promoters in enhancer marks provides an 
additional argument for the involvement of lincRNAs in the regulation of 
transcription in cis. By investigating the epigenetic regulation of lincRNAs, we 
observed both positive and negative correlations between DNA methylation and 
gene expression (expression quantitative trait methylation [eQTMs]), as 
expected, and found that the landscapes of passive and active roles of DNA 
methylation in gene regulation are similar to protein-coding genes. However, 
lincRNA eQTMs are located closer to TSSs than are protein-coding gene eQTMs. 
These similarities and differences in genetic and epigenetic regulation between 
lincRNAs and protein-coding genes contribute to the elucidation of potential 
functions of lincRNAs.