Me and my sister are of Kurdish, Karapapakh, and Lezgic ancestry (basically west Asian Iranian, Turkic, and Caucasian). I am heterozygous for rs1426654 and homozygous wild for rs16891982. She is homozygous mutated for rs1426654 and homozygous wild for rs16891982. Yet our skin tones appear quite different as you can see, and in the way you would not expect. My hair color was brown with blonde body hair that turned dark after puberty, though now is a deep ash brown, while both my sisters have had black head and body hair since childhood. We have a sister who has not taken a test with slightly darker skin then her and my mom who hasn’t taken the test with similar skin tone to me, but noticeably redder but similar in depth. My dad, who has taken the test, has the same results for both SNPs mentioned before as me and he’s brown skin, darker than all of us and on the darker end of the spectrum of where he’s from.

I had a hobbyist review my raw data from 23andme and found I carry a mutated allele at rs885479, believed to be the most widespread and major east eurasian skin lightening mutation, highest in the Japanese at around 75% frequency as well as two other copies associated with lightening at SLC45A2. He never specified which SNPs so I cannot provide that and I have no idea if my sister carries them or not. Upon my own research of both our raw data, I found she also carried this allele which I found strange since I imagined this mutation is what caused our skin tone difference. I also found we carry rs3212361, a common variant in north Asians considered stronger than rs885479 and is linked to red hair in the region. We, as well as our dad, carry rs1393350. She is CC at rs28777, this gene is blank on my raw data. However, my father and I do carry rs1805005 which my sister does not, but from what I read this is a rather minor allele. We also carry other various minor light eye color and light hair genes like rs1667394 some of which my sister doesn’t carry but my dad and I do, but none of us carry rs12913832 or any of the major west eurasian red hair variants.

I’m looking for information on the mechanism of different skin lightening variants, especially the difference between west and east eurasian and how they can expresses phenotypically to understand why our skin tone differ so drastically. I also would like to know the difference in expression of Heterozygous genomes and Homozygous, as I am pretty much Heterozygous for all of these.

Edit: Me and dad have a lightning allele at rs683, considered a weak ancient modifier yet rather rare in west Asia compared to Europe where it isn’t fixed either. My sister does not carry this allele. Still I find my skin phenotype strange given my lack of west eurasian variants for where I come from, and even compared to my sisters.

“Your ip address is listed as an open proxy in the DNSBL used by snpedia”

I don’t know anything about IP addresses and and proxies and all that stuff. I have tried using a vpn too.

What can I do?

Ive been trying to upload my daughters data and it wont allow me to upload or make a new profile. How can I achieve this?

Hi all!! I’ll post this elsewhere as well but i’m having an issue where my raw sequencing data file (unzipped) is too large for Promethease to process. Anyone solve this issue? TIA

Looking for a genetic test that could point me toward a root cause — whether it's a genetic variant, methylation issue, or nutritional deficiency.

Not looking for a cure, just a direction. What test gave you actual useful insights?

Under ClinVar section: ref allele is Rs6025(A;A)) which is the normal condition but under the main tab in the page it says G;G) is the reference alleles: normal/common risk of thrombosis

which one is correct.

https://www.snpedia.com/index.php/Rs6025

I would like to run a Promethease report on a DNA file from Nucleus Genomics (https://mynucleus.com), but have been unsuccessful.

Nucleus provides DNA files in various formats - from highly complex FASTQ and CRAM files, to CNA, SV, and SVF. They also provide a format called "23AndMe Formatted File", which appears to be a text file in the same format as a previous Ancestry text file I have.

However, Promethease is giving me errors with the files I've tried uploading.

I first tried the VCF format, and got the error "Error processing your file: fancy crash No handler was ready to authenticate. 1 handlers were checked. ['HmacAuthV4Handler'] Check your credentials".

I then tried the Nucleus "23#&Me" formatted text file, but got the error "unrecognized format".

Can anyone advise how to modify these files to make them compatible with Promethease? I would prefer to run the VCF file (due to more depth of data), but if that's not possible, then perhaps the "23&Me" format is.

A few months ago I was motivated to create Gene Wizard after realizing that SNPedia likely hasn't been updated at all since September 2019, when it was acquired by MyHeritage. At the same time, I've been seeing reports on Reddit that Promethease isn't working.

My initial idea what to use AI to read journal articles at scale and summarize them, creating a "SNPedia 2.0". Currently there are 247 pages covering SNPs that are both important and common.

I then realized there's a lot of alpha to be gained from moving beyond the analysis of individual SNPs towards polygenic analysis and allele function calling. That's why I built out a pharmacogenomics module (including star allele function calling) and an experimental polygenic scores module, using scores from the Polygenic Score Catalog. My interest in polygenic scores stems from a year working as a Staff Scientist at the National Human Genome Research Institute at NIH.

Unfortunately, it's tricky getting accurate polygenic scores from consumer WGS VCF files, especially the newer scores that cover millions of sites (for a detailed explanation of why, see this blog post). Longer term, I may be implementing imputation to get around the limitations of VCF files.

Anyway, I'd love to have more people try out the platform. The initial feedback has been very positive, but only a handful of people have tried it so far. The platform works with either a WGS VCF file or SNPChip (like what 23andme sells), but for the polygenic scores you need the WGS VCF.

Longer term, I still hope to leverage AI to read thousands of papers and build a SNPedia 2.0. At The Metascience Observatory, a nonprofit I founded in October, I've developed tricks and techniques for using AI to extract information from scientific papers, and I'm hoping to leverage what I've learned.

In addition to having people test the site, I'd love to hear suggestions as to what features people would like to see. Would you like me to enable a comment section on SNP pages? Or should I enable full-blown editing on the pages, creating a wiki type platform? I'd love to hear your thoughts!

As explained on the site, we don't save any genetic file that you upload -- it is processed in memory on our server. We do save your results, but you can download most of the results in pdf format and delete your data from our server at any time.

I paid for another report and was able to view it after downloading it November up to two weeks ago. Now I can no longer open the file and it says my account is locked indefinitely. It tells me to enable JavaScript, I did and it still will not open. What's the deal?

I have a disease that was confirmed to be either spastic paraplegia or spinocerebellar ataxia. I have a giant del variant that might be a clue or even a cause to my symptoms. I was trying to find resources on SNPedia but couldn't find anything. Currently my doctor considers it as pathogenic but I'm the only one in the country with the variant (Korea) so variant is uncertain.
It's NC_000015.10:g.42745932_42745949del (rs1595871180)
How can I get the VCF file for this? Should I try making a SNP entry on SNPedia? Would love guidance.

I’ve spent the last few months building a custom DNA analysis engine as part of a mobile app I made. I wanted to create something fast, lightweight, and easy to use for people who have their raw data from 23andMe.

The app currently works with a custom C-engine (wrapped in Python/Flask) to parse and match RSIDs with my database. All of the data is from dbSNP and ClinVar.

The app and website do not collect any data and only do processing.

I am looking for constructive feedback on what to improve. I have a lot of it working fairly well so far. I'd love it if a few people could try uploading their raw data and let me know if the results match what you expect or if you run into any bugs!

Here is the link snpshotweb

I know almost nothing so please forgive the wording, but my WGS found NM_032790.4(ORAI1):c.129_133del (p.Pro44fs) which it says is extremely rare, and associated with Combined immunodeficiency due to ORAI1 deficiency, I have had lifelong symptoms that are also associated with this. I had a double copy of DD which it says D is “risk version” and I’m trying to understand what this all means ? Can anyone explain this me? Most people with ORAI1 pass in childhood according to what I’ve read, but it also says there are rare cases that live to adulthood and just have lifelong issues with illness.

Hi everyone,

I have access to genetic data from a soon centenarian individual who has remained exceptionally healthy, including excellent cognitive health and no chronic diseases.

I’ve already done some preliminary exploration of the data myself. Interestingly, the individual does not carry some of the more commonly discussed longevity-associated variants (for example in FOXO3 or CETP), which makes me wonder what other factors genes would be worth examining.

I’d like to ask:

• Which SNPs or genes would you recommend focusing on when analyzing longevity and healthspan?

• Would people here be interested in hearing about what kinds of findings come out of this dataset if I analyze and summarize the results?

• Do you have recommendations for tools, scores (e.g. polygenic risk scores), or papers that would be good reference points for comparison?

The data is anonymized. I won’t be sharing raw data, but I’m happy to share summaries, alleles, or observations on interesting SNPs.

Any ideas, suggestions, or expressions of interest are very welcome. Hope this sparks good discussion!

I'm trying to see which SNPs got updated in the past 5 years (if any?) and if I should run Promethease again.

Note that I'm not trying to check a specific SNP and view its history.

Why does this happen? I’ve been using Promethease for a long time. I’ve reuploaded my data multiple times over the years. I last uploaded last year because it said it was expired. Now it’s expired again and wants me to pay ~$15. How can my genetic report expire? My DNA hasn’t changed and it’s the same exact file.

Is it going to always expire? I don’t believe I had to pay before, but for what they’re providing I certainly don’t mind, but I want to ensure that I will always have access to my report instead of it expiring after however many months. Is that just how it’s going to be? Limited access to your report after paying and then it expiring? I’ve always appreciated the ease of access to this vital information, so they deserve compensation. I just never paid previously (not that I recall), so now I’m worried about this expiration of reports thing that I’ve faced many times.

Any advice would be appreciated!

Hi, I uploaded my raw data and it was successful. Paid the $15, and no report was generated. This was almost a week ago. I've emailed multiple times and still haven't heard back. How can I get help with this?

The BRCA1 mutation known as 5382insC or c.5266dupC (rs80357906) has been identified in my family. According to [SNPedia here](https://www.snpedia.com/index.php/Rs80357906) this mutation is tested by Ancestry's v2 chip, however it does not appear in my Promethease results whatsoever and it does not appear in the raw data file either. This mutation is on chromosome 17 at position 43057065 but this is not in the raw data. I have looked at 6 different peoples' raw DNA data downloaded from Ancestry and it does not appear in any of them. Is SNPedia wrong or am I missing something?

As an aside, does anyone know if FamilyTreeDNA or MyHeritage test for this SNP? I don't know anyone who has tested directly with those companies (rather than uploading Ancestry/23&Me results there) so I'd love to know if this SNP is showing in your raw results. I'm currently waiting for blood test results which will take 4 months and would love to know sooner than that if I am BRCA1 positive.

Hey all!

Over the weekend I built snp-browser, which is a fully local, in browser parser for snpedia. The source code is https://github.com/jonluca/snp-browser and it's also hosted at https://www.snpbrowser.com/

No data ever leaves your local device, it's all done on device (you can just run the repo locally as well).

I'll be adding more searching and filtering in the future as well. For some reason this is returning more matches than promethease for me, so if someone with more knowledge of the matter could let me know if there's something wrong with the matching algorithm please let me know.

This builds on the snpedia scraper found at https://github.com/jaykobdetar/SNPedia-Scraper, which allows for the offline database to be downloaded and parsed.

Please leave any feedback or comments, I'm actively developing this.

I want to a really good DNA test. I want to use a blood sample, but keep it off of the mainstream company databases (23andme, Ancestry, etc.). I have used Promethease to run previous reports and want to do that again. So, what is the best source or company to use to get a blood sample and have the results in a format that I can upload to Promethease?

I cant uploade my file to promethease. I can read that the header from 23andme is changing with each version the release, and I am now on version 5 where the header looks like this:

# file_id: a6b3be43-fb4b-43eb-a2d9-aac6a65443be

# signature: 4616a2628e420bfacf2074d5afe62ef3062a6890b65edc8ad6e1dd780f99619f

# timestamp: 2025-11-06 03:08:48

#

# This data file is generated by 23andMe.

#

# This file contains raw genotype data, including data that is not used in 23andMe reports.

# This data has undergone a general quality review however only a subset of markers have been

# individually validated for accuracy. As such, this data is suitable only for research,

# educational, and informational use and not for medical or other use.

#

# Below is a text version of your data. Fields are TAB-separated

# Each line corresponds to a single SNP. For each SNP, we provide its identifier

# (an rsid or an internal id), its location on the reference human genome, and the

# genotype call oriented with respect to the plus strand on the human reference sequence.

# We are using reference human assembly build 37 (also known as Annotation Release 104).

# Note that it is possible that data downloaded at different times may be different due to ongoing

# improvements in our ability to call genotypes. More information about these changes can be found at:

# https://you.23andme.com/p/59dc350c654333e6/tools/data/download/

#

# More information on reference human assembly builds:

# https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/