i am using the population based case-control association test for a complex disease (myopia), and i am in the candidate gene approach but not whole-genome.
i have genotyped all the tagged SNPs in the gene ( pairwise tagging by hapmap, r2>0.8, mirror allele frequency >0.2), after i did association test for each SNPs independently,
my boss asked me to do the haplotype analysis too, but i dunt know the meaning of haplotype analysis,
why it is needed? i have done association test for each SNP already.... is this a meaningless test?
i have search for a lot of journals, they said haplotype is a combination of alleles that inherited as a single unit and is being used for geneticist to locate or confer the disease variant???
why somethimes single SNP assocaition test apper negative, but haplotype assocaition test appear positive???
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