Table 2.

Summary of the main variant annotation tools for non-coding DNA regions

Name	Uses	Main data sources	Advantages	Limitations	Reference
RegulomeDB	Prioritization of functional variants, using a score based on the number of elements with which the variant overlaps	ENCODE, Roadmap Epigenomics Project	Includes information from numerous functional annotation sources	The scoring system can be difficult to interpret	[103]
HaploReg	Annotation of variants in LD, located within or next to regulatory elements	ENCODE, GTEx, Roadmap Epigenomics Project	Allows the identification and mining of causal variants in LD that affect regulatory sites	Functional annotations are not updated periodically	[106]
FunciSNP	Identification and prioritization of putative regulatory SNPs	ENCODE, Roadmap Epigenomics Project	Large data queries are fast to perform	A minimum knowledge of R is needed for its use	[107]
rVarBase	Annotation of regulatory variants that are involved in transcriptional and post-transcriptional regulation	ENCODE, Roadmap Epigenomics Project	Uses annotations of numerous regulatory features, easy to use, intuitive website	Results summary can be initially confusing, i.e. a SNP can appear annotated with both strong and weak transcription	[108]
FunSeq2	Prioritization of cancer-associated SNVs in non-coding DNA	ENCODE	Can annotate and prioritize variants directly from BED or VCF files and the analysis can be customized	It is specifically designed to annotate cancer-associated variants but not for variants associated with other diseases	[109]
ENlight	Annotation of GWAS variants and analysing their putative effects through plot visualization	GWAS, ENCODE, GTEx	Plot system is useful to visually identify causal variants and the analysis can be customized	Functional annotations are not updated periodically	[110]
INFERNO	Characterization and prioritization of regulatory variants in different tissues	GTEx, FANTOM5, Roadmap Epigenomics Project	Prioritize variants by calculating an empirical p-value	Large Web queries take a long time to complete	[111]
Cepip	Prioritization of gene regulatory variants using tissue-expression data and predicted scores	GTEx, ENCODE, scores from different prediction tools	Integrates the effect of multiple chromatin states to identify and prioritize functional regulatory variants	A minimum knowledge of the command line is needed for its installation and use	[112]
GEMINI	Annotation of non-coding variants by integrating chromatin information for different cell types	ENCODE	Incorporates a workflow that automatically annotates variants from VCF or pedigree files	Requires command line use and lacks regulatory features in comparison with some other annotation tools	[113]
OncoCis	Prioritization and annotation of cis-regulatory somatic variants in cancer samples	ENCODE, Human Epigenome Atlas, Jaspar, FANTOM5	The annotation procedure is more rigorous in comparison with other tools for identifying cis-regulatory mutations and it can be applied for identifying cell type-specific variants	It is specifically designed to annotate cancer-associated variants but not for variants associated with other diseases	[114]
SuRFR	R package that integrates annotations from different resources to prioritize functional regulatory SNPs	ENCODE, FANTOM5	Short execution times and higher data confidentiality in comparison with Web-based tools	The user must be familiar with the R programming language	[115]