Where necessary, we attempted to find the most likely intervals for the remaining unplaced loci or to compare all possible orders for indefinite regions.
Markers that had earlier been removed from the map due to their destabilizing effect on locus order (i.e. those with jack-knife values <90%) were assigned to the most likely intervals on the framework map and were referred to as 'attached' markers.
The markers were placed to the most-likely interval with the 'try' command and a minimum LOD of 3.0.
We suggest that, in the same vein, the hunt for distal variants causing transcriptional mis-regulation of a disease-associated gene should first be performed in the TAD in which the gene in question lies, as this is the most likely genomic interval to harbor its long-range control elements.
However, an increased risk was seen in the subgroup of non-smoking women ≥60 years old (though with broader confidence interval), most likely due to reduced power in our analyses compared to when analyzing presence (≥1 copy) vs. absence (0 copies) of GSTM1.
AN0112, encoding GeaA, was identified as the most likely candidate in this interval and was sequenced (primers 20 27).
There is no significant difference in the first dS interval, most likely because of residual polymorphism and/or a low mutation rate in SO and UP clusters.
