Custom (checkbox selected) data

Besides volumes of regulatory/epigenomic data, there are many other datasets that may be useful to test specific biological questions. Such datasets may not fit within the systematic schema of GenomeRunner, and are handled separately (see Makefile)

We put several databases accessible through the checkboxes on the front page. Their description, and potential use, is shown in the table.

Genome annotation category	Description	Experimental question: Are the SNPs of interest...
coriellVariants	Coriell Cell Line Copy Number Variants, split by cell types	... enriched in CNVs, and in which cell type?
CpG-xxx	Model-based CpG islands	… enriched in CpG sites?
dgvVariants	Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del), split by variant type	... enriched in CNVs, or other types of structural variations?
GERP-xxx	Genomic Evolutionary Rate Profiling elements	... enriched in evolutionary constrained regions?
gwasCatalog	NHGRI Catalog of Published Genome-Wide Association Studies, split by disease/trait types	... enriched in known disease-specific SNPs?
knownAlt	Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes, split by splicing type	... potentially disrupt a specific type of alternative spliced regions?
ncRNAs	C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase, split by ncRNA type	... associated with a class of non-coding elements?
nestedRepeats	Repeating Elements by RepeatMasker, split by repeat class	... enriched in regions of low complexity, and in which class? Classes include: 'Short interspersed nuclear elements (SINE), which include ALUs', 'Long interspersed nuclear elements (LINE)', 'Long terminal repeat elements (LTR), which include retroposons', 'DNA repeat elements (DNA)', 'Simple repeats (micro-satellites)', 'Low complexity repeats', 'Satellite repeats', 'RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)', 'Other repeats, which includes class RC (Rolling Circle)', 'Unknown'
super_enhancers	Super-enhancers in the control of cell identity and disease. Article	... enriched in cell type-specific super-enhancer regions?
tfbsEncode	Transcription Factor ChIP-seq Clusters V3 (161 targets, 189 antibodies) from ENCODE, split by TFBS name	... potentially disrupt a specific experimentally defined transcription factor binding site?
tfbsConserved	HMR Conserved Transcription Factor Binding Sites, split by TFBS name	... potentially disrupt a specific computationally defined transcription factor binding site?
UCNEs	UltraConserved Noncoding Elements from the UCNE base	... potentially disrupt ultra conserved elements
VMRs	Variably Methylated Regions (VMRs) and CpG sites (CpGs) Article	... potentially alter regions/CpGs variably methylated across normal tissues, hence, affecting cell/tissue identity?

Please, request any other genome annotation data you'd like to have