There are unbalanced genomic data of multiple domains for different cell types/tissues. For example, a lot of data were provided by ENCODE tier 1 cell lines (GM12878, K562, H1 human embryonic stem cells), whereas the data were few on tier 3 cell lines. It may potentially affect the quality of our annotation when applying GWAS3D pipeline to the cell lines having fewer data available. We therefore specially selected the 16 cell types, which included enough chromosomal looping data (5C or ChIA-PET or Hi-C) and important transcriptional markers data (H3K4me1, H3K27ac, DHSs, EP300 and CTCF). To cope with tissue/cell type limitation, we added a ‘without tissue/cell type restriction’ item in cell type selection option by merging the genomic profiles of three ENCODE tier 1 cell lines. Because the aforementioned three cell lines contain dynamic transcription signals from human normal adult cells, cancer cells and embryonic stem cells. In the future, we will continuously update the number of tissue/cell type when enough data are available for that cell line.
