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Old 04-30-2010, 05:15 AM   #1
Location: Shanghai China

Join Date: Apr 2010
Posts: 11
Default how to fetch the snp allele frequency?


I now need a txt file with several columns, which contains the rs ID of snp, frequency of each allele. I was told to download the SNPAlleleFreq.bcp file from ncbi. But i don't know exactly what each column tells about, and who to fetch the snp allel freq. So i need some help.

thanks very much
dzmtnvmt is offline   Reply With Quote
Old 05-18-2010, 06:27 AM   #2
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Location: Germany

Join Date: May 2010
Posts: 101


if you haven't found another way yet, I'd recommend downloading the snp130 table from the UCSC genome browser. I suppose you'd like to have SNPs for the latest human genome? Then go to
and download snp130.txt.gz

A description of the columns is available in the "Tables"
when you select from the dropdown menu
group: Variations and Repeats track: SNPs (130)
table: "snp130"
and then hit "describe table schema"

Hope this helps
epigen is offline   Reply With Quote
Old 01-24-2011, 08:54 AM   #3
Location: cinci

Join Date: Apr 2010
Posts: 66

I have the same question, I am interested in frequency information from dbsnp132. I have chromosomal positions and rs#s and want to get frequency information. My goal is to filter out common snps since 1000genomes data is supposed to discover rare variations <1%.
husamia is offline   Reply With Quote
Old 06-21-2011, 03:44 AM   #4
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Location: sweden

Join Date: Jul 2010
Posts: 4

Hello! I checked one biallelic SNP in this database (snp131) to determine allele freq. I found an average heterozygosity of 0.5. I guess this is because there is no data on allele frequency? Or is it actually 0.5? In that case allele frequency should also be 0.5 according to hardy-weinberg?

Thanks for your help!
megnetz is offline   Reply With Quote

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