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I want to add the frequencies of the genotypes to a baseline of raw DNA data I've got from the DNA testing companies 23andMe, Ancestry and MyHeritage (tested at all). All in build 37 human genome.

Where can I find that information? Checked HapMap project to no avail, can't align with the rsId or positions used in the text files.

Thanks in advance for your help

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gnomad is probably the most comprehensive allele frequency database that exists at the moment.

Depending on how many variants you need to query, you can either manually input them into the search bar, or if you have a lot more, then you can also directly download the vcfs under the downloads tab.

The default for V2 gnomad set is on the gr37 build.

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  • $\begingroup$ I have to check over a million SNP's - so manual isn't an option. Thanks for the link, checking it out with the smallest chromosome first. $\endgroup$ – a4xrbj1 Jul 28 at 6:00
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The largest number of samples is at the dbSNP database. To view frequencies of a single rsID in a web browser, for example, rs11950646, use the following URL:

https://www.ncbi.nlm.nih.gov/snp/rs11950646#frequency_tab

The dbSNP has more samples to calculate the frequency than gnomad, at least for this rsID.

If you need to automatically process multiple rsIDs, as you said, for the whole genotype file that you got from the companies like 23andMe, you can download a VCF with allele frequency data from https://ftp.ncbi.nih.gov/snp/population_frequency/latest_release/ and write a script to automatically process the data and make the output in a format you want. If you only need frequency of some rsIDs within a single chromosome, you can download the whole database for that chromosome from https://ftp.ncbi.nih.gov/snp/latest_release/JSON/ and will find the data in the JSON files, each file for each chromosome (plus the mtDNA). Look for the "frequency" field.

If you are not engaged to write scripts, and just wish to interactively browse various rsIDs in context of a frequency, you can upload your genotype file to selfdecode.com - it is a convenient, albeit a paid service.

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