Missing 23andMe SNPs: What To Do

Written by Samantha Odake, BS | Last updated:


Have you ever tried to search for a SNP in your 23andMe raw data, only to find it wasn’t there? You’re not the only one. So, what should you do when you discover missing 23andMe SNPs in your DNA file? Let’s find out.

23andMe DNA Test

23andMe is a popular DNA service that offers ancestry, health, and trait analysis based on samples provided by customers using their at-home DNA testing kits.

After the user provides the sample, 23andMe uses genotyping to analyze the DNA and generate reports. The current DNA kit from 23andMe tests around 650,000 SNPs.

23andMe SNP list

23andMe does not provide a full list of SNPs tested, seeing as they are in the hundreds of thousands. They do provide a list of all the reports available, which include:

  • 50+ ancestry reports
  • 30+ trait reports
  • 10+ health predisposition reports
  • 5+ wellness reports
  • 40+ carrier status reports

23andMe+ subscribers have access to an additional 30+ reports.

How to find SNPs in 23andMe

Users can browse their raw data directly from the site. You can search by gene, marker (rsID), or genomic position, and 23andMe will display your genotype. Another option is to click on a chromosome to view the associated markers.

Missing 23andme SNPs

You can also download your raw data from 23andMe and then browse the text file that will be provided to you.

But, what should you do when you find missing 23andMe SNPs in your file?

Why are there missing 23andMe SNPs in my file?

To date, there are more than hundreds of millions of SNPs that have been discovered in humans. So, it’s no surprise that you might discover missing 23andMe SNPs in your DNA file.

Most genotyping companies are only testing around 500,000 – 900,000 SNPs, possibly leaving out many that are important to give you more accurate insights into your health and ancestry.

Fortunately, there is technology available today that allows companies to predict variants at non-genotyped SNPs based on genotyped variants. This means you can take your raw DNA data and upload it to other websites if you want to find more information about your missing 23andMe SNPs.

What to do about missing 23andMe SNPs

If you want to learn more from your DNA, you can upload your raw data to companies like SelfDecode, or get a SelfDecode DNA kit.

SelfDecode uses a process called genetic imputation to analyze important parts of your genome to figure out parts that are not known, which allows them to increase the number of SNPs analyzed. SelfDecode’s imputation uses cutting-edge AI and machine learning to predict SNP genotypes and is based on many other variants.

Using genetic imputation, SelfDecode turns the ~750,000 SNPs that their world-class Illumina GSA DNA kit analyzes into over 83 million additional variants with an accuracy rate of 99.7%. This allows SelfDecode to analyze over 100x more of your genome than other leading DNA testing companies.

SelfDecode then uses this data to figure out which of these variants affect your health and translate this into polygenic risk scores that tell you how your genetic risk for different health conditions and traits. SelfDecode’s algorithm also predicts the best health recommendations to counteract your risk based on your genes.

Another standout feature SelfDecode offers is the ability to search their database of 83M+ SNPs to discover your genotype, which is great for those who want to dive deep into their genes. Below you can see a SNP table containing an example MTHFR genotype result. As you can see, this search alone returns over 26,000 results.

Missing 23andMe SNPs MTHFR

In addition to the gene & SNP database with over 83M entries, users who sign up for SelfDecode get access to 300+ DNA health & trait reports, comprehensive diet & nutrition and fitness reports, personalized health plans based on DNA results, and more.

The reports provide health recommendations that are personalized and prioritized according to your results. Users can view their genetic predispositions and how each recommendation helps specific health issues.

SelfDecode also specifies how each recommendation helps a health condition or trait based on your DNA results. Users can click on the gene or SNP to find out more information about them. You can view a sample below.

SelfDecode also offers cutting-edge ancestry insights including ancestry composition, mitochondrial ancestry, and other detailed reports.


23andMe is a popular DNA testing company that can provide insights into people’s health and ancestry. However, it might happen that you search for a SNP in your 23andMe data, only to find it missing.

In this article, we’ve reviewed what to do when you come across missing 23andMe SNPs. Companies such as SelfDecode use a process called genetic imputation to accurately predict your genotype for over 83M SNPs. Then, SelfDecode uses this data to calculate your polygenic risk scores for hundreds of health conditions & traits and provide personalized health recommendations based on your DNA.


About the Author

Samantha Odake

Samantha Odake

Samantha is an engineer turned writer with a passion for helping people.


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