CNV categories that were investigated for role in transcriptional expression.

Three classes of CNVs were investigated. The WTCCC CNVs were divided into two groups, according to whether they were tagged (r2≥0.80) by a local (i.e., within 1 MB) SNP from imputed WTCCC1 data and genotyped WTCCC2 data from both the Affymetrix and Illumina arrays (see http://www.wtccc.org.uk/wtcccplus_cnv/masterCNVlist.final.README.txt). The third group contains CNVs assayed in HapMap LCLs (Conrad et al.) that were determined to be different from those in the WTCCC set.