The identify candidate causal SNPs and pathways (ICSNPathway) analysis identified seven candidate SNPs, five genes, and seven pathways, which together revealed seven hypothetical biological mechanisms.
The functional analysis result would facilitate to understand all kinds of main features (coding, non-coding and eQTLs) of the pathway related SNPs and select candidate causal SNPs, which will further contribute to the interpretation of GWAS data.
Using single marker analysis, we evaluated the effect of each SNP marker and identified the potential causal SNPs or chromosomal regions contributing to variation in the ability to germinate anaerobically.
However, causal SNPs are usually not genotyped.
High LD level assures nearly perfect match between imputed and causal SNPs, and thus retains substantial portion of the true effect size, resulting in power reaching nearly to that by testing on causal SNPs under all MAF intervals.
Further pursuit of functional and causal SNPs within chromosome 6p21.3 and replication of our results are warranted.
Such SNPs likely indicate enrichment with causal SNPs that do not reach the genome-wide significance level because of their small effect size or low allele frequency [11].
In order to interpret this pattern, we calculated the MAF of imputed and causal SNPs, and the LD measure D' between them.
Medium LD level, on the other hand, could retain some association signal through imperfect LD, resulting in a power that was lower than that on causal SNPs.
The 100 causal SNPs were chosen independently in each replicate.
where C is the set of all possible causal SNPs.
