From: Functional annotation signatures of disease susceptibility loci improve SNP association analysis
Name | Annotation class | Description |
---|---|---|
MAF1..4 | Minor Allele Frequency | Natural spline basis for MAF |
funcIntron | dbSNP Function Class | Indicator that variant is intronic. |
funcNg3 | dbSNP Function Class | Indicator that variant is near-gene-3. |
funcNg5 | dbSNP Function Class | Indicator that variant is near-gene-5. |
funcNonsynon | dbSNP Function Class | Indicator that variant is missense or nonsense. |
funcSynon | dbSNP Function Class | Indicator that variant is synonymous. |
funcUTR | dbSNP Function Class | Indicator that variant is in the 3 ′ or 5 ′ UTR. |
PhyPC1..4 | phyloP Evol. Cons. Score | First 4 PCs for PhyloP data. |
IndelInd | DGV Regions | Indicator that SNP is in the region of a known in–del. |
CNVInd | DGV Regions | Indicator that SNP is in the region of a known CNV. |
InvInd | DGV Regions | Indicator that SNP is in the region of a known inversion. |
BrPC1..18 | ENCODE Super–Track | PCs of Broad promoter/enhancer ChIP–seq data. |
CalPC1..11 | ENCODE Super–Track | PCs of CalTech transcription level RNA–seq data. |
logDNase | ENCODE Regulatory Super–Track | DNaseI hypersensitivity cluster log(score). |
TFBSfreq | ENCODE Regulatory Super–Track | SNP in ChIP–seq TFBS region(s) – count. |
logTFBS | ENCODE Regulatory Super–Track | SNP in ChIP–seq TFBS region(s) – log(TFBS score). |
ORegInd | Open REGulatory ANNOtation DB | Indicator that SNP is in ORegAnno DB. |
PPh2Prob | PolyPhen–2 | Probability that SNP is damaging. |
RegDBcat | RegulomeDB | RegulomeDB category. |