Physical map for distal chromosome 7
Distal Chr 7 from ~120 and 132 Mb may modulate App
Physical map of variation in App expression in brain on distal Chr 7 (a blow up of the whole-genome map on the previous slide).

Notes:
1. You can now see that the X-axis is on a physical scale of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.
2. The small irregular colored blocks and marks toward the top of the map mark the locations of genes superimposed on the physical map. Neighboring genes are offset slightly in the vertical axis for display purpose. Note one region of very high gene density from about 120 to 123 Mb.
3. The orange hash marks along the X-axis represent the number of single nucleotide polymorphisms that distinguish the two parental strains (C57BL/6J and DBA/2J) from each other. We call this the SNP seismograph track (see Glossary for more details). Regions with low numbers of SNPs have closely matched sequences and are less likely to contain QTLs.
4. As before, the thin red line shows the additive effect size. By convention the positive values signify the D alleles are associated with higher expression of App in this region of Chr 7 than the B alleles. The maximum effect size is about +0.20 log2 expression units per D allele. The differences been the BB and DD genotypes (BB and DD because each strain has two alleles; one per chromosome) is therefore about 2^0.4 = 1.32 or a 32% increment in DD relative to BB at this locus.
5. If you scroll just under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO YYY MbÉ..Ó  These physical maps are zoomable, a feature we will exploit to evaluate candidate genes in this QTL interval.