Thanks for posting those two references.
I've listed a paragraph from the first paper and it reads ...
"As expected, SNPs in the MHC on chromosome 6p were strongly associated with ankylosing spondylitis (rs7743761 P = 5.0 × 10 to the power of -304). Association was evident across a very broad region surrounding the MHC, including five SNPs lying in a 153-kb region at 26.0–26.1 Mb from the p-telomere (5.4 Mb from HLA-B), which achieved P < 10−5. The most associated SNP in this region was rs3734523 (P = 1.6 × 10−6). However, conditional logistic regression analysis suggested that this was unlikely to represent a separate independent association because conditioning on five of the most significant SNPs from the MHC (rs7743761, rs2596501, rs3915971, rs2516509, rs1265112) caused the association to disappear (P = 0.27)."
This indicates that rs7743761 is on Chromosome 6 - which contains the MHC and specifically HLA B antigens. It becomes very difficult to identify independent risks factors (that is other than B27) on Chromosome 6 because of the concept of linkage disequilibrium.
Put simplistically, if there is a high risk SNP on or near the MHC on chromosome 6, the association with AS might disappear if you can somehow control for the presence or absence of HLA B27.
For a discussion on linkage disequilibrium refer to Wikipedia.