Summary of the 20 sequenced deletion variants.

Column 1: exact genomic position (UCSC March 2006 genome build) of each deletion, determined from sequencing results; Column 2: size of each deletion (bp) and 3 breakpoint insertions; Column 3: number of samples carrying each deletion (��1 copy), identified by aCGH or imputed using CNVhap; Column 4: number of chromosomes sequenced�Csamples with homozygous deletions are scored twice, not all deletions missed by aCGH but imputed by CNVhap were sequenced; Column 5: name of genes (if any) overlapped by deletions; Column 6: introns/exons overlapped by deletions; Columns 7 & 8: these show whether the upstream and/or downstream deletion breakpoints are located within/adjacent to any repeat sequence elements. * indicates Alu elements with poly-A tails flanking the breakpoint; Column 9: max r2 scores for LD with surrounding SNPs within 50 kb window for each deletion; Column 10: significance values for r2 scores. For the deletion on chromosome 19, the analysis was first performed assuming that the reference sample had a copy number of 2 (i.e. homozygous undeleted), and then re-calculated on the basis that the reference was a heterozygous deletion at this loci. The number in brackets refers to the calculation assuming a heterozygous deleted reference.