DNA methylation is commonly found as epigenetic switches of regulatory elements. Accordingly, the methylation level of CpG dinucleotides in an eRNA locus is usually associated with the eRNA expression level. Here we privide all the statistically significant associations between eRNA expression and CpG methylation identified in our study.

Interestingly, the eRNAs were found to have Prognostic power comparable to mRNAs, or even beyond that for some complex traits, such as the response to immunotherapy. Here we provide a systematic analysis on the eRNA prognostic power in all 32 TCGA cancer types. The Cox-regression model was used to detect the association between the OS (overall survival), PFI (progression-free interval), or DSS (disease-specific survival) with either the absolute (RPKM) or relative changes (log2RPKM) of each eRNA's expression.

Remote enhancers conduct regulatory functions by looping to their target promoters. This can be revealed using Hi-C interaction data. Here we provide all co-expressed eRNA/gene pairs connected at the level of 3D-chromatin structure according to the 3D Genome Browser

Focal somatic copy-number alterations (SCNA) identified with the GISTIC software with an FDR < 0.05 by the TCGA Pan-Cancer analysis consortium are potential cancer drivers. A total of 3,678/1,047 non-coding amplification/deletion SCNAs involving at least one eRNA locus are found to contain no gene or ncRNA.

We inferred the transcription factor (TF) occupancy in each eRNA locus using the cistrome ChIP-seq mega-dataset. This table provides the eRNA loci, overlapping ChIP-seq peaks in the cistrome database, and the tissue/cell type of ChIP-seq signals.

eQTLs are SNPs genetically associated with the cellular amount of a given mRNA (or protein), usually indicating the local existence of enhancer/regulator of the interested mRNA. Our integrated analysis show that the nucleosome-mediating transcription of eRNA is a strong indicator of the probability of a nearby common SNP being a GTEx eQTL. This table provides all eRNA loci with 1k-Genome common SNPs being eQTLs of their potential target genes.

A signature of 164 eRNAs was found to be associated with response to immunotherapy. This table provides the list of these 164 eRNAs, their potential target genes inferred from eQTLs, and their cellular functions related to T-cell expansion revealed by GSEA.

This table provides a list of all the Somatic mutations detected by TCGA on the TCeA eRNA loci. Notably, TCGA uses whole exome sequencing (WES) and thus covers only a subset of the eRNAs. More data will be released in future update.