Question: find alternative allele frequency from 1000 Genomes
gravatar for star
4.4 years ago by
star240 wrote:

I have SNPs position and rsID for 500 SNPs, I would like to find alternative allele frequency for them based on 1000 Genomes? would you please help me.

ucsc ensembl 1000 genomes ncbi • 2.0k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by star240
gravatar for WouterDeCoster
4.4 years ago by
WouterDeCoster44k wrote:

You could do that by using Biomart from Ensembl

  1. Go to
  2. Database = Ensembl variation
  3. Homo Sapiens Short Variants
  4. Filters: General Variant Filters: Filter by Variant Name
  5. Attributes: VARIANT ASSOCIATED INFORMATION: 1000 Genomes global Minor Allele Frequency (all individuals)
ADD COMMENTlink written 4.4 years ago by WouterDeCoster44k

Thanks a lot. I know that but I want to find Alternative allele frequency.

ADD REPLYlink written 4.4 years ago by star240

Yes, so the minor allele may not be the alternative allele such as C in rs123. C is the minor allele and the reference, not the alternative allele. If you add the 'ancestral allele' and 'variant alleles' in Attributes, you can find out which one is the alternative, and if the latter is not the minor, you can deduct the MAF from 1 (or 100%) to get the frequency for the alternative allele (AAF, alternative allele frequency). You could also try the Ensembl REST API using the POST variation endpoint. Finally this FAQ may be useful too.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Denise CS5.1k
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