I would like to compare the allele frequency of a list containing 3000 SNPs related to a given trait between my population and 1000 genome populations (super populations). For my population, the SNPs derived from whole genome sequencing of about 1000 individuals. But, due to missing genotypes and some quality control done at previous steps, the number of individuals (so the total allele counts) is not the same at all SNP positions, however as I checked, it (the total allele count) is the same at all positions for 1000 genome population. As I read, the fisher’s exact test can be used to compare allele count among the population for finding SNPs with significantly different allele frequency, yes? I also aware of the simple Fisher's test for one SNP in R, but I don’t know how I can do it for a list of 3000 SNPs and get the adjusted p-value for each SNP. Could you please help me out on this issue?
P.S. As I’m a basically biologist, please kindly suggest/advise me any point that should be considered for doing the analysis.