LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs

BMC Bioinformatics

Table 2 Sources of disease-associated SNP annotation

Annotation	Item	Source	Description
SNP Summary	General Information	BioQ	BioQ provides query and documentation tools for genomic relational databases.
	Genome Wide Association	BioQ
	1000 Genome SNP	BioQ
	LD Plot	BioQ
Genomic Mapping	Reference Gene	UCSC	Genes and Gene Prediction Tracks\RefSeq Genes\refGene;
	Ensemble Gene	UCSC	Genes and Gene Prediction Tracks\Ensembl Genes\ensGene;
	Known Gene	UCSC	Genes and Gene Prediction Tracks\UCSC Genes\knownGene;
	Small RNA	UCSC	Genes and Gene Prediction Tracks\sno/miRNA\wgRna;
	MicroRNA Target	UCSC	Regulation\TS miRNA sites\targetScanS;
	TFBS	UCSC	Regulation\TFBS Conserved\tfbsConsSites;
	Enhancer	VISTA Enhancer	Tissue specific human enhancers;
	Insulator	CTCFBSDB	Vertebrate genomic insulators;
Evolution	SNP and Gene positive selection	SNP@Evolution	A hierarchical database of positive selection on the human genome;
	Conserved Functional RNA	UCSC	Genes and Gene Prediction Tracks\EvoFold\evofold;
	Conserved Elements	UCSC	Comparative Genomics\Conservation\Mammal EI;
Gene Co-Expression	3-way SNP-expression Associations	SNPxGE2	Human SNP–expression associations
Disease Association	OMIM gene	OMIM	Online Mendelian Inheritance in Man;
	DGV gene	DGV	Structural variation in the human genome;
	GAD gene	GAD	Genetic Association Database;

Note: BioQ: http://bioq.saclab.net; UCSC: http://genome.ucsc.edu; VISTA Enhancer: http://enhancer.lbl.gov; CTCFBSDB: http://insulatordb.uthsc.edu; SNP@Evolution: http://bighapmap.big.ac.cn; SNPxGE2: http://lambchop.ads.uga.edu/snpxge2/index.php; OMIM: http://www.ncbi.nlm.nih.gov/omim; DGV: http://dgv.tcag.ca/dgv/app/home; GAD: http://geneticassociationdb.nih.gov/cgi-bin/index.cgi.

ISSN: 1471-2105