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
Dear,

First you need to make sure which transcript you are interested. Keep in mind that the same SNP will have different cDNA coordinates between transcripts. Also you need to watch out for the genome version. Because g coordinates will also vary between different genome versions. Moving from your example, you can go to www.ensembl.org and write in the search CD2AP. You will see that the golden transcript is <a href="http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000198087;r=6:47477789-47627263;t=ENST00000359314">ENST00000359314</a> with 629 aminoacids. Now go to biomart at http://www.ensembl.org/biomart . Here select ensembl variation database, than select SNPs and Indels. Next from the left click on filters and go to gene associated filters. Here paste your gene ID which is ENSG00000198087. Next go to the attributes tab and select the coordinates you want (genomic, mRNA, coding sequence..etc) Download your results and you will have your SNPs.

I hope this helps,