Paralogous genes in genome-wide association studies?
There is no literature report saying such a thing. However, I did a cursory check for GWAS study on neuroblastoma. 


Selected SNPs with p-value>0.05
Converted p-values to a score —  -log10(p-value)
Mapped the SNPs to genes while calculating cumulative score for a gene


I just sorted the genes based on their names, assuming that many paralogs have similar names. I know it is not the right way to go about it. However, I found many similar named groups in the list. 

Now the next step is find actual paralogs and to score the cumulative score for a paralog-group. This is a little task:


Get sequences of the genes
Run a BLAST search to find paralogs
Assign genes to groups and find scores


I can share the file with genes and scores. I would, however, continue only if someone is actually interested in pursuing this — this could be a research paper.

PS: If you want the file just comment your email id. Some IT admin idiot has blocked rapidshare/4shared etc