Correct way to group the mice samples based on the haplotype of a single location

[Saikat Bandyopadhyay]

I am analyzing bulk RNA seq data generated from the DO. I have genotype information for these and I have performed QTL analysis for some skeletal traits. 

There are some of the locus with interesting QTL associations, I am wondering how can I efficiently group the mice based on the haplotype of the locus and perform DESeq kind of comparison. 

I wantt to do this for a specific locus or a group of locus, for example for a locus on chrosome1:152-155 Mb. I would really appriciate the suggestions.