When I search for this online I get answers such as substitutions, deletions, insertions etc. But I mean in the sense that I have been reading different terms infront of the word SNP such as: lead SNP, tag SNP, sentinel SNP, indirect SNP, direct SNP, secondary SNP, imputed SNP etc.

From my understanding lead/tag/sentinel are all the same (SNP with lowest P value in a locus, representing the variance in that section). An indirect SNP is also a lead/tag/sentinel SNP and indirect because these have not been genotyped but are in LD with the genotyped SNP + having that they have the lowest P value. Also a secondary SNP is a indepedently correlating SNP, and is specifically independent from the tag SNP? Is there a resource defining these sort of categories? Apologies if this is misinformed, I have been trying to learn about GWAS from different studies, and would appreciate any help to clarify this.


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