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haplotype analysis - help help help help (May/21/2010 )


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???


May be this could be helpful for you