Can anyone please help me I will be grateful
I want to reconstruct haplotype using PHASE Program. I wish to know whether Human population specific snps (for particular gene) or snps close/adjacent to my focus snp are required to be used for Haplotype reconstruction.
with PHASE you can use any SNP you want (at least 2 of course) to reconstruct haplotypes.. what do you mean by population specific snps? to infer haplotypes you need at least two SNP which are polymorphic..
If you already have a SNP of interest ( as appears from your question), then you should get genotypes of the flanking region, select all of the polymorphic loci in that region (you may decide on the length of flanking region) and then reconstruct haplotype using PHASE.
You do not need to include info about near SNPs if you have already two or more. If you want to check population-specific SNPs or haplotypes, you can do it easily using 1000 genomes
For constructing haplotype, minimally 2 SNPs suffice.
IF, the population that you are interested in is already REPRESENTED in available databases, eg 1000 genomes, then you can just go ahead with 2 of the reported SNPs for haplotype construction. You need NOT to go with the flanking region information.
But, if you are considering a population that is ETHNICALLY DIFFERENT from those submitted in the available databases, then you might have to consider getting SNP information of the flanking region by sequencing. Because ethnically different populations may differ in the levels of variation. Even there are chances that few of polymorphic loci will be monomorphic in ethnically different population.
Do you already know where is the promoter region for your gene of interest? If yes, then start of promoter position or the TSS (transcription start site) may help you decide on the length of upstream region (may be few KBs upstream of ATG of gene). For deciding on the downstream region, you may have to cover till the 3'UTRs are covered (may be few KB downstream).
If you do not know the promoter or UTR details then you have to visit some database to know that. Few commonly used sites are :
http://www.ncbi.nlm.nih.gov/gene
http://www.genecards.org
Search by gene name and navigate through the hyperlinks provided in the resultant gene page. It should provide you the coordinates for up- or downstream.
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