proxy SNPs for Fine mapping

Question

[dizue]

Hi, I have a question regarding to fine mapping to identify credible SNPs.

For example, if a disease has 60 loci that have been previously found by GWAS study, and I want to run a fine mapping on these loci. However, for some loci there are very limited or no proxy SNPs for the tagged variants, in this case does this mean fine mapping can not be performed?

Or does this mean the tagged variant is the causal variant?

[Brian Bushnell]

There are also indels, structural rearrangements, CNVs, variable-length tandem repeats, racial/ethnic/dietary factors, and a host of other things that may be linked to the array SNP. So a lack of other nearby SNPs does not mean the tagged variant is causal, and the GWAS results do not even necessarily mean that the locus is relevant.

[dizue]

thanks. i got what you say, but in case of running fine mapping using existing GWAS locus I suppose without nearby SNPs it is impossible to do so.