Does anyone know where could I find a comprehensive list of human CNV regions? I am working with 1000G variants and want to filter out variants within CNV regions, to see whether some pattern change or not.

Thanks,  
Federico
The 1000 Genomes Consortium recently published an integrated SV/CNV map for the 1000 Genomes phase 3 data:

http://www.nature.com/nature/journal/v526/n7571/full/nature15394.html

As a VCF file:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz

Alternatively, Decipher also has a population CNV map in tab-delimited format:

https://decipher.sanger.ac.uk/files/downloads/population_cnv.txt.gz