Summary of functional characteristics.

*All SNPs are annotated in a binary fashion indicating the presence or absence of a functional characteristic, except for the conservation scores, for which the SNPs are assigned a quantitative score.**The DNase Clusters v2 file was created by combining the UW and Duke DNase I data that have been uniformly processed and replicates merged. Stringent (FDR 1% thresholded) peaks of DNase I hypersensitivity from uniform processing by the ENCODE Analysis Working Group were applied. Grouping the UW and the Duke DNase I hypersensitive variables are not equivalent to the DNase Clusters v2 file, and thus we used the latter to represent DNase I hypersensitive sites in the clumped analysis due to the substantial efforts made to combine the data meaningfully.