PhenCode (Phenotypes for ENCODE; http://www.bx.psu.edu/phencode) is a 
collaborative, exploratory project to help understand phenotypes of human 
mutations in the context of sequence and functional data from genome projects. 
Currently, it connects human phenotype and clinical data in various 
locus-specific databases (LSDBs) with data on genome sequences, evolutionary 
history, and function from the ENCODE project and other resources in the UCSC 
Genome Browser. Initially, we focused on a few selected LSDBs covering genes 
encoding alpha- and beta-globins (HBA, HBB), phenylalanine hydroxylase (PAH), 
blood group antigens (various genes), androgen receptor (AR), cystic fibrosis 
transmembrane conductance regulator (CFTR), and Bruton's tyrosine kinase (BTK), 
but we plan to include additional loci of clinical importance, ultimately 
genomewide. We have also imported variant data and associated OMIM links from 
Swiss-Prot. Users can find interesting mutations in the UCSC Genome Browser (in 
a new Locus Variants track) and follow links back to the LSDBs for more detailed 
information. Alternatively, they can start with queries on mutations or 
phenotypes at an LSDB and then display the results at the Genome Browser to view 
complementary information such as functional data (e.g., chromatin modifications 
and protein binding from the ENCODE consortium), evolutionary constraint, 
regulatory potential, and/or any other tracks they choose. We present several 
examples illustrating the power of these connections for exploring phenotypes 
associated with functional elements, and for identifying genomic data that could 
help to explain clinical phenotypes.