# SNP-phenotype association analysis only using the SNPs on a specific gene

I know that the GWAS association p-value threshold is 1e-8. This makes sense because in GWAS, you make ~1 million hypothesis (i.e. use that many SNPs in the association test). However, let's say I do not do genome-wide analysis but only use the 100 SNPs from a specific gene to check for association with my phenotype. Then, do you think a raw p-value of 1e-4 (which becomes 1e-2 after multiple hypothesis correction) is a reliable p-value to come to a conclusion that there is an association between that SNP and the checked phenotype? Obviously, if I checked all 1 million SNPs instead, this p-value would be insignificant after correction, but I am not checking 1 million SNPs, as I mentioned.