1000 Genomes Project data is available at both Ensembl and the UCSC Genome Browser.
Ensembl provides consequence information for the variants. The variants that are loaded into the Ensembl database and have consequence types assigned are displayed on the Variation view. Ensembl can also offer consequence predictions using their Variant Effect Predictor (VEP).
You can see individual genotype information in the Ensembl browser by looking at the Individual Genotypes section of the page from the menu on the left hand side.
The 1000 Genomes raw sequence data represents more then 30,000x coverage of the human genome and there are no tools currently available to search against the complete data set. You can, however, use the Ensembl or NCBI BLAST services and then use these results to find 1000 Genomes Project variants in dbSNP.
Information relating to ancestral alleles is available for phase three of the 1000 Genomes Project. The work on annotating ancestral alleles is described in Section 8.3 of the supplementary material of the publication accompanying that work.
The final 1000 Genomes phase 3 analysis calculated consequences based on GENCODE annotation and this can be found in the directory: release/20130502/supporting/functional_annotation/
Ensembl can also provides consequence information for the variants. The variants that are loaded into the Ensembl database and have consequence types assigned and displayed on the Variation view. Ensembl can also offer consequence predictions using their Variant Effect Predictor (VEP).
Data from the 1000 Genomes Project has now been analysed multiple times and on different reference assemblies. In addition, further data sets have been generated and analysed. These studies, therefore, use different data, different reference assemblies and different methodologies, which can lead to different variant calls being made.
The studies that IGSR makes data available for are listed with their accompanying publications in our data portal. The publications can provide further details.