. 2017 Nov 10;93(9):657–676. doi: 10.2183/pjab.93.042

Table 1.

Available computer tools for in silico functional analysis

Location of the variant	Notes	Tools	URL	Refs
Exon (Non-synonymous variants)	Prediction of the protein structure damage by the mis-sense variants	Polyphen2	http://genetics.bwh.harvard.edu/pph2/	46
Exon (Non-synonymous variants)		MuPIT	http://mupit.icm.jhu.edu/MuPIT_Interactive/	47
Splice site	Evaluate the functional change by splicing	Human Splice Finder	http://www.umd.be/HSF/	48
Gene expression regulatory region	Summarize the regulatory elements for gene expression	HaploReg v4.1	http://archive.broadinstitute.org/mammals/haploreg/haploreg.php	55
	Summarize the regulatory elements for gene expression	Regulome DB	http://www.regulomedb.org/	56
	Comprehensive information	UCSC genome browser	http://genome.ucsc.edu/index.html	57
		ZENBU	http://fantom.gsc.riken.jp/zenbu/	58
	Prediction of TF binding	TRANSFAC	http://www.gene-regulation.com/pub/databases.html	59
3′UTR	Prediction of miRNA binding to 3′UTRs	PolymiRTS	http://compbio.uthsc.edu/miRSNP/	61
3′UTR	Prediction of miRNA binding to 3′UTRs	RegRNA	http://regrna2.mbc.nctu.edu.tw/	62
Coding, splicing isoform	Prediction of mRNA folding	RNAsnp	http://rth.dk/resources/rnasnp/	64
Coding, splicing isoform	Prediction of mRNA folding	mfold	http://unafold.rna.albany.edu/	65
All	Database of e-QTLs	GTEx portal	http://gtexportal.org/home/	70, 71