The 1000 Genomes Project shares some samples with the HapMap project; any sample which starts with NA was likely part of the HapMap project. In the pilot stages of the project HapMap genotypes were also used to help quality control the data and identify sample swaps and contamination. Since phase 1 the HapMap data has not been used by the 1000 Genomes Project, and all genotypes were independantly identified by 1000 Genomes.
The 1000 Genomes Project submits all its variants to archives like dbSNP or the DGVa. If it hasn’t yet made it to dbSNP this means it is likely to be a new site which we haven’t yet submitted. There may also be some old sites which we subsequently discover to be false discoveries which we then suppress.
As far as our overlap with the HapMap site list goes, The majority of HapMap SNPs are found in the 1000 Genomes Project, there will be a small number of sites we fail to find using next generation sequencing but most sites from HapMap which aren’t found by the 1000 Genomes Project will be false discoveries by HapMap. There are a lot of SNPs from the 1000 Genomes Project and other next generation sequencing projects which won’t be part of HapMap as HapMap is based on an older genotyping technology when such rapid variant discovery using sequencing was not possible.