A list of the CNV's used by the GATK is available on the Broad FTP site:
"The current best set of known indels to be used for local realignment (note that we don't use dbSNP for this anymore); use both files:
1000G_phase1.indels.b37.vcf (currently from the 1000 Genomes Phase I indel calls) Mills_and_1000G_gold_standard.indels.b37.sites.vcf"
dbVar is a repository of structural variation (http://www.ncbi.nlm.nih.gov/dbvar). We routinely remap variants submitted on older assemblies to the newest ones (when we can). Data is organized by study so it is straightforward to get the data you want, both 1000 genomes and other studies.