Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs

BMC Bioinformatics

Table 1 Navigator table interface of ASB SNPs on a chosen chromosome

chrom	Pos	rsID	Counts					cCRE	Motif Enrichment	Genome Broswer link	Variant Viewer link	GTEx	GWAS
chrom	Pos	rsID	Ref	Alt	Ref	Alt	p.val		Motif Enrichment	Genome Broswer link	Variant Viewer link	GTEx	GWAS
chr1	196723542	rs381974	A	G	0	34	4.38E–08	CTCF-only, CTCF-bound	–	Genome Broswer	Variant Viewer	–	–
chr1	111197723	rs599134	C	G	0	22	7.54E–06	dELS, CTCF-bound	YES	Genome Broswer	Variant Viewer	ENSG00000162777.16	Reticulocyte_fraction_of_red_cells
chr1	159821674	rs60205880	G	C	0	21	1.21E–05	CTCF-only, CTCF-bound	YES	Genome Broswer	Variant Viewer	–	–
chr1	153617778	rs9330298	C	A	19	0	3.16E–05	pELS, CTCF-bound	YES	Genome Broswer	Variant Viewer	ENSG00000160678.11	–
chr1	30783058	rs4147103	T	C	2	26	6.78E–05	dELS, CTCF-bound	YES	Genome Broswer	Variant Viewer	ENSG00000162511.7	–
chr1	211649200	rs12741252	G	C	17	0	8.53E–05	dELS, CTCF-bound	YES	Genome Broswer	Variant Viewer	–	–
chr1	89085986	rs11589629	G	C	19	1	0.0003	CTCF-only, CTCF-bound	YES	Genome Broswer	Variant Viewer	ENSG00000213516.9	–
chr1	150067621	rs2027349	A	G	0	9	0.0065	PLS, CTCF-bound	–	Genome Broswer	Variant Viewer	ENSG00000266472.5	–

This is an example of an HTML report for the ASB SNPs located on chromosome 1 (chr1), with the reference SNP identification number (rsID), as indicated. This interactive summary report also lists the position (pos) of an allele, read counts [e.g., reference count (ref count) and alternative count (alt count)], p values, cis-regulatory element (cCRE), motif enrichment and analysis, as well as the hyperlinks to multiple databases, including the Genome Browser, Variant Viewer, GTEx portal, and GWAS

ISSN: 1471-2105