LD Select 1.13 – Patterns of Linkage Disequilibrium Analysis

LD Select 1.13


LD Select analyzed the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2.


At each round of selection, the binning algorithm identifies the single SNP which exceeds the threshold r2 with the maximum number of other SNPs, and sets this group of SNPs as a bin. Then each SNP within the bin is analyzed to determine whether it exceeds the threshold r2 with all other SNPs in the bin. All SNPs in a bin that meet this criterion are designated as TagSNPs. Only one TagSNP needs to be typed per bin.


Dr. Deborah Nickerson’s lab at the University of Washington




  • Linux / Windows / Max OS X
  • Perl


LD Select



Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. Selecting a maximally informative set of single-nucleotide polymorphisms for association analysis using linkage disequilibrium. Am J Hum Genet. 2004 Jan;74(1):106-20. Epub 2003 Dec 15.

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