Intuitively we would expect that inclusion of a causal SNP as a covariate would reduce the residual linkage due to IBD to zero (Almasy et al., 1999), but this is an area of active research. After each SNP marker was separately tested in the variance component model, it was found that inclusion of the number of minor alleles of any single SNP was not able to explain all variation in the SHAS phenotype. When considering the dataset after removing family 44, the peak LOD score was 3.36. The marker that lowered this LOD score the most (by 1.21 LOD units) when included as a covariate was rs10776687, the marker located closest to the linkage peak. Other SNPs lowered the LOD score by lesser amounts, as seen in the Table 2 below. Combined linkage and association analysis indicates that no single locus tested is likely to be the only causal allele. When testing haplotypes, none of the three haplotypes were able to completely account for the linkage signal.
