Dear All,
I have conducted haplotype analysis to create LD block for my SNPs after GWAS. However, I find some significant SNPs outside the LD blocks, any probably explanation or education. Thanks
Are their physical positions inside the LD block? If that is the case, have you checked for the population structure? Maybe these SNPs are in haplotypes that are frequent in one population, but not in the other.
Beside this, maybe they were excluded by some quality metrics.
an other possibility is that they are false positive significant SNP.
fred
LD block means they inherit together as a block from the donor but not necessarily linked to each other. If something is outside the block means they did not inherit together and possibly independently.
We just need to know if an SNP marker is associated with the target trait. Since it is associated, it is more valuable. This SNP acts independently based on the LD blocks, so it may not have pleiotropic effect.
- Badges
- Science method
- Similar topics
- Mathematics
- Statistics
- Statistical Techniques
- Meta-Analysis