It should be noted that the WTCCC CNVs included in our study reflect certain limitations. Indeed, as the WTCCC study itself explicitly noted [8], a large proportion (nearly 60%) of the candidate list of putative CNVs could not be reliably assigned copy number classes from the combination of experimental assay and analytical approaches; it is estimated that only about half of these are not polymorphic [8]. Particularly, nearly 6,500 such putative polymorphisms were excluded from subsequent analyses, as they were called with a single copy number class. It is of course possible that our conclusions may not generalize to these CNVs. Furthermore, eQTL mapping in microarray-based studies in LCLs is likely to yield only a subset of the eQTLs that will be identified using more refined methods in a variety of human tissues. The present study also has little conclusive to say about low frequency variants. Despite these current limitations, the annotation system we implemented in SCAN should prove useful to other investigators and seeks to be as comprehensive as possible by providing functional information for the most extensive map
