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How to use SNPedia – The Wikipedia For SNPs and Powerhouse for Promethease

What is SNPedia?

SNPedia (snpedia.com) is like Wikipedia but for single nucleotide polymorphisms (SNPs). The information presented on SPNedia is curated from the latest peer-reviewed scientific papers. Researchers and genetic enthusiasts can use SNPedia to learn about the effects of DNA variations in health and diseases.

What are SNPs?

Our entire genome is made up of many genes that carry out certain functions inside the body. Each gene is again made up of many single nucleotides. In total, each person has 3 billion of these nucleotides. Because we all come from a common ancestor, we share 99.9% of these nucleotides. The remaining 0.01% variation comes from these variable SNPs. They not only make us different from each other, but also give us different likelihoods of developing certain medical conditions.

Learn more about basic genetics and how SNPedia works on their official FAQ page.

How are SNPedia and Promethease related?

Promethease is a third-party DNA analysis tool for health genetic information. If you upload your own DNA data to Promethease, it then retrieves information from SNPedia to help you estimate the risks of developing certain diseases. In other words, Promethease is what you use to get a health report, but the information on the report is powered by SNPedia. 

How to use SNPedia?

You can explore any SNP inside the SNPedia database through Promethease or SNPedia directly.

If you have a report from Promethease, you can click on a specific SNP and be taken to the wiki page of this SNP on SNPedia. 

(A SNP on Promethease that you can click on)
A SNP on Promethease that you can click on

Clicking on the SNP from Promethease is the same as searching for this SNP manually on SNPedia.

SNPedia search
You can also search for the same SNP on SNPedia

Next, you will see that (T;T) is a variant for the gene RNASEL, which is located on Chromosome 1. Having this particular variant is associated with a 1.5x – 2x increased risk for cervical cancer, breast cancer, and head and neck squamous cell carcinomas (HNSCC). Because of this increased disease risk, SNPedia classified its Repute as ‘Bad’

To learn more about what this SNP location, SNPedia directs you to the main wiki page for rs3738579. Here, you will read that it represents a SNP in the RNASEL gene. One study in 2008 reported that variations of this SNP are associated with different risks for certain cancers.

You could also see the other variants that others may have for this SNP. For example, (C;T) is a variant associated with decreased risk for these certain cancers. Because a decreased risk is supposed to be protective, this variant has a Repute of ‘Good’ and is marked in green.

An important thing that SNPedia did for us here is to evaluate how much evidence there is. In this case, the paper that provided the information was published over a decade ago. No follow-up or replication studies have been done to corroborate the results. Thus, SNPedia warns you to treat this result as preliminary and not to jump to conclusions.

You may have also noticed that all three variants of the same SNP have a Magnitude of 1.1. What does this mean? 

SNPedia magnitude is a subjective rating of how interesting people think of a piece of information. It doesn’t have any health-related meaning but is purely a rating by users on Promethease and SNPedia. The lowest rating is 0, which means not interesting. Higher the value, more interesting it is to the average user.

What SNPs can you explore on SNPedia?

SNPedia currently contains 110684 SNPs in the database. These are the ones that have significant medical consequences revealed by research. Of course, there are many more SNPs in our genome, but these are the ones worthy of recording based on existing research.

What SNPs to explore are completely up to you. Most users use filters on Promethease to find the most important SNPs that could affect their health. Then, they explore these SNPs on SNPedia. 

Check out our guide on Promethease to learn about filters.

How can you get more information about a SNP?

If you are interested in exploring a SNP further, you could delve into the literature that SNPedia has pointed you to. In those papers, you could get a better understanding of how big the study was, what tests were performed and how researchers interpreted the data.

Apart from researching on your own, you could also join discussions with others. There are many threads on Reddit regarding SNPedia and various SNPs. In fact, one of the founders of SNPedia Mike Cariaso himself is a user on the subreddit r/SNPedia: a wiki about DNA variations. You could potentially get answers from him and other experts.

Commonly asked genes on SNPedia

Autism genes

SNPedia also has curated information pages for genes and disorders that people commonly ask about. For example, Autism is a complex disorder that is associated with many SNPs. To better explore genetic associations with Autism, you could see a curated list of genes and SNPs on SNPedia.

ApoE4

There are many people interested in the ApoE4 gene variant as it is famous for increasing the risk for Alzheimer’s disease. SNPedia offers a comprehensive wiki page on APOE4 Community that has lots of good information on our current knowledge of this topic.

MTHFR

Another commonly asked about is MTHFR, mainly because of some unfounded claims from supplement companies. SNPedia’s founders created an informative page on MTHFR that can help people clear up the confusions and worries.

Other popular genes on SNPedia

If you are a newbie to SNPedia and are lost in the data, here is a list of popular genes to start exploring! Apart from those, there are some interesting SNPs that can even affect your behaviours and emotions!:

  • rs90925 can influence how aggressive and antisocial you are, if you are a woman.
  • rs53576 is linked to emotions like empathy, loneliness, more sensitive parenting techniques and lower risk of autism.
  • rs4680 determines the level of dopamine in your prefrontal cortex. One variant can make you a warrior who is more resilient. The other variant has an opposite effect, which can make you a worrier.
  • rs1800955 is an adventure gene that can determine whether you like to seek novelty.

Summary

In summary, SNPedia is a great wiki resource for anyone who is interested in learning about SNPs and how they may contribute to diseases. SNPedia is the powerhouse of Promethease, which scans your raw DNA to retrieve SNPs that may be interesting to explore on SNPedia. If you are looking for a full review on Promethease, be sure to check out our comprehensive guide on Promethease!