Hi Haojam, I would recommend doing an intersection in the table browser:
clade: Mammal genome: Human assembly: your choice group: Variation and Repeats track: a SNP track table: snp### Next, click on "create" for intersection and select your gene prediction track of interest at the top of the page. Select the option "All SNP records that have any overlap with ..." and click "submit". Finally, click "get output" to get the BED file with all SNPs located within human gene transcript regions. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 1/5/11 7:08 PM, 하오잠 로 wrote: > Dear Sir/ Madam, > I would like to find the SNPs density located in human gene transcript > regions i.e. 5'UTR, 3'UTR, CDS or coding exon. For this I have already > downloaded the 3'UTR, 5'UTR and CDS from the UCSC table genome browser. Could > I do it with SNPBLAST or ENTREZ SNP Database but SNPBLAST is not supporting > what I want. Could you please tell me how would I proceed to obtain my goal. > I would be glad for your kindness and assistance. > > Warm regards, > Haojam Rocky > Ph.D. scholar > Seoul National University College of Medicine > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
