Transmission Disequilibrium Test (TDT).

The top 35 associated SNPs are listed together with the surrounding genes defined by either Grail (www.broadinstitute.org/mpg/grail/) or the Genome Browser (http://genome.ucsc.edu/). The disease associations are acquired from the “Catalog of Published Genome-Wide Association Studies” (http://www.genome.gov/gwastudies/). For PLINK: genotypes were imputed if any of the posterior probabilities were >0.95. For expTDT: T and U are the expected transmission counts (based on all the posterior imputation probabilities). NPL – the most significant Non Parametric Linkage (NPL) p-value for the same locus as the SNP. P-values below 0.05 are marked in italics. T and U – the number of heterozygous parents who transmit the alleles A1 and A2, respectively. T/U – transmission odds based on the expected transmission counts. *the marker in the set of SNPs from the linkage analysis closest to the marker in the SNP column (when this marker was not run in the linkage analysis). aclosest known gene. located >500 kb from associated SNP.