Hello all, I am new in plink analysis

I have Map file and I know that location (start /end) of ***CD2AP ***gene on chromosome 6 has base pairs 47,477,745 to 47,627,262

How can I use physical position column in MAP file to extract SNPs of this gene

Any help will be appreciated
plink cannot process isolated `.map` files; do you have an accompanying `.ped`? (If you don't, it might be simpler to write a short script for this job.)

If you do, 

    plink --file [.ped/.map filename prefix] --chr 6 --from-bp 47477745 --to-bp 47627262 --write-snplist --out [output filename prefix]

should give you the list you're looking for.