Since so many new SNPs are present in the 1000 Genomes data and latest builds of dbSNP, a large number of websites such as F-SNP and the SNP Info Web Server's function prediction module do not have annotation predicting the function of said SNPs. Going beyond things like PolyPhen or SIFT estimates of synonymous/non-synonymous intronic/intergenic, is there an integrated pipeline which can give details on things like: Is the SNP in a TF binding site?
miRNA binding site?
Other regulatory region?
eQTL for genes?
The last of these is unlikely. F-SNP only runs up through dbSNP build 126 and the SNP Infor Webserver only covers later HapMap builds?
What is the latest integrated pipeline for annotating SNP function for 1000 Genomes variants with rs numbers? Is there one? Or must one use a collection of tools? What do those of you with a long list of SNPs from the more recent dbSNP builds do to annotate these things?