Regulatory polymorphisms play important roles in determining phenotypes and disease susceptibilities through perturbing gene expression. After genetic markers with LD have been mapped, an important task is to evaluate their functional importance based on the identification of regulatory regions and specific regulatory elements. Here we introduce the leading bioinformatics tools and invaluable resources to facilitate the functional analysis in silico. We focus on promoter prediction, modeling,

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... ediction of transcription factor binding sites and identification of sequence elements important for splicing regulation. These tools are becoming increasingly accurate and powerful to guide experimental investigations and to transform correlated alleles into mechanistic understandings.