Table 1.
Description of annotations organized in GWASdb
| Level | Item | Description | Reference |
|---|---|---|---|
| Snp Summary | General information | dbSNP 132 annotation for each GV | dbSNP-Q (32) |
| Genome-wide association | Manual curation and collection | GWASdb | |
| 1000 Genome SNP | SNPs and indels in 1000 Genomes Project 1049 subjects (May 2011 release) | 1000 genome project | |
| LD plot | LD data from HapMap Phase II+III | HapMap | |
| Genomic mapping | Reference gene | Gene annotation from NCBI Refseq | NCBI Refseq |
| Ensemble gene | Gene annotation from Ensemble | Ensemble | |
| Known gene | Gene annotation from UCSC | UCSC | |
| Small RNA | snoRNA and miRNA annotations from UCSC | UCSC | |
| MicroRNA target | TargetScan generated miRNA target site predictions | UCSC | |
| Transcriptional factor binding site | Transcription factor binding sites conserved in the human/mouse/rat alignment, based on transfac Matrix Database (v7.0) | UCSC | |
| Enhancer | Human Enhancer verified by experiment | VISTA Enhancer DB (33) | |
| Insulator | CTCF binding site database for characterization of human genomic insulators | CTCFBSDB (34) | |
| Regulatory effects | Transcriptional factor binding site affinity | GV affinity of TFBS prediction based on fold energy change with PWM scanning | GWASdb, TRANSFAC (35) JASPAR (36), UniPROBE (37) |
| MicroRNA target site affinity (for Pita) | GV affinity of miRNA target prediction based on fold and hybrid energy change for PITA top targets | GWASdb, PITA (38) | |
| MicroRNA target site affinity (for Miranda) | GV affinity of miRNA target prediction based on hybrid energy change for miRanda targets | GWASdb, miRanda (39) | |
| Splicing site affinity | GV affinity of splicing site prediction | ssSNPTarget (40) | |
| Amino acid substitution | Non-synonymous SNP functional prediction | Non-synonymous GV deterioration prediction | dbNSFP (41) |
| Evolution | SNP positive selection | The estimation of FST and heterozygosity of GV for positive selection | SNP@Evolution (42) |
| Gene positive selection | The estimation of FST and heterozygosity of gene for positive selection | SNP@Evolution | |
| Conserved functional RNA | Conserved functional RNA, through RNA secondary structure predictions made with the EvoFold program | UCSC | |
| Conserved elements | Conserved elements produced by the PhastCons program based on a whole-genome alignment of vertebrates | UCSC | |
| Gene expression | Three way SNP expression association | Gene co-expression relationships with GV effect | SNPxGE2 (43) |
| Disease association | OMIM | Online Mendelian Inheritance in Man | OMIM |
| DGV | Curated catalogue of structural variation in the human genome | Database of Genome Variants | |
| GAD | Archive of human genetic association studies of complex diseases and disorders | Genetic Association Database |