Genetics and Beyond – The Transcriptome of Human Monocytes and Disease Susceptibility
Figure 4
The loci affecting CDKN2B expression and CAD on chromosome 9p21 are independent.
The lead SNP rs1333049 generally reported at the CAD locus was not present on the Affymetrix 6.0 array, we therefore selected its best proxy, rs10757272 (position 22078260, r2 = 0.9 with rs1333049), using SNAP (https://www.broadinstitute.org/mpg/snap). Positions of genotyped SNPs are shown using a green link and position of the proxy SNP, rs10757272, is represented by a green triangle. The red curve reflect the –log10(P-value) for the association between SNPs and CDKN2B expression. The LD (r2) between pairs of SNPs is shown at the bottom of the figure using a range of colors between white (r2 = 0) and black (r2 = 1). The CDKN2B and CAD-associated SNPs are located in different blocks of LD strongly suggesting that the genetic effects on CDKN2B expression and CAD are independent.