As you all know the 1000G sites are a sheer freaking delight to navigate.
But I understand from here: http://www.1000genomes.org/page.php?page=announcements that the exonic sequences are available, but only cover 8,140 exons in 906 "randomly selected" genes: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/technical/working/20100511_snp_annotation/pilot3/annotated.CHB.final.P3.
The paper just released has info on the 1000G pilot: http://www.1000genomes.org/bcms/1000_genomes/Documents/nature09534.pdf
But in addition to mining the variants in LD with those significant in our GWAS using haploxt: http://www.sph.umich.edu/csg/abecasis/GOLD/docs/haploxt.html
what is the best way to determine if any variants in LD map to exons and cause coding changes? Is there a tool like Polyphen through which they could be run in batches?