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For SNP, gene, and exon positions:
For SNP, gene, and exon positions:
*[http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP position] via the [http://genome.ucsc.edu UCSC Genome Browser]
*[http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP position] via the [http://genome.ucsc.edu UCSC Genome Browser]
*[http://www.ncbi.nlm.nih.gov/RefSeq/ Gene and exon positions] via the [http://genome.ucsc.edu UCSC Genome Browser]. We filtered SNPs that map to more than one location or where no allele matches the reference sequence
*[http://www.ncbi.nlm.nih.gov/RefSeq/ Gene and exon positions] via the [http://genome.ucsc.edu UCSC Genome Browser]. We filtered SNPs that map to more than one location or where no allele matches the reference sequence.
For annotation:
For annotation:
*We used various sources including RefSeq Genes (refFlat), TFBS Conserved (tfbsConsSites), and Conservation (phaseConsElements44wayPlacental), all available from the [http://genome.usc.edu UCSC Genome Browser].
*We used various sources including RefSeq Genes (refFlat), TFBS Conserved (tfbsConsSites), and Conservation (phaseConsElements44wayPlacental), all available from the [http://genome.usc.edu UCSC Genome Browser].
*[ftp://ftp.hapmap.org/hapmap/recombination/2008-03_rel22_B36/rates/ Recombination rates from HapMap]
*[ftp://ftp.hapmap.org/hapmap/recombination/2008-03_rel22_B36/rates/ Recombination rates from HapMap].
== Input ==
== Input ==
