Please excuse the basic question but I am new to GWAS. It is my understanding that haplotypes are blocks of DNA sequence where the bases therein are always coinherited because (as yet) the blocks of DNA do not undergo recombination. Haplotypes can be characterised by key tagSNPs
In a GWAS you find haplotypes or tagSNPs associated statistically with a particular trait. As a general point, how does the distance between a causal variant of the trait and the tagSNP affect the resulting association? I thought that, by definition of a haplotype, all of the bases in the region are ALWAYS coinherited with the tagSNP (otherwise it wouldn't be a haplotype) so the distance of the causal SNP from the tagSNP does not affect the strength of the association. In other words, excluding other confounding factors like environment etc, would all SNPs inside a haplotype have the same signal strength if they had the same association with the disease?
Are the signals from SNPs additive? Lets say a haplotype had 2 SNPs associated with a disease, would their signals 'add up' to give a stronger signal?
Is it possible that SNPs outside the haplotype may sometimes segregate with the haplotype and cause weak signals for the haplotype?