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Table 1 Annotations used to construct the functional signatures

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.
  1. Definitions of the 54 variables appearing in the prior model for association status arranged by type/class of annotation.