Table 1 Annotations used to construct the functional signatures

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.