Table 2.
SNP type and its function score
| Region | Description | Score |
|---|---|---|
| Conserved region of 8-genome alignment | Human /chimp /mouse /rat /dog /chicken /fugu /zebra_fish conserved region from 8-genome multi-alignment | Use multiple alignment score(1) |
| Conserved transcription factor binding site (TFBS) | contain the location and score of transcription factor binding sites conserved in the human/mouse/rat alignment | Use original raw score(2) |
| CpG island | CpG island may be potential regulatory region | Use CpG island expectation score(3) |
| microRNA gene | microRNA involves in gene regulation | Score(4) is normalized to the range between 0 and 1 |
(1)
UCSC phastCons scores for multiple alignments (Siepel and Haussler, 2005)
(2)
from Penn State University Genome Alignment and Annotation Database (http://gala.cse.psu.edu/gala/downloads/hg17/tfbinding_sites/)
(3)
from UCSC human annotation database table for CpG island (http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/cpgIslandExt.txt.gz)
(4)
from UCSC human annotation database table for microRNA (http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/wgRna.txt.gz).