Hey everyone! All of you who have tested through 23andme or any other genotyping or genome sequencing company, will be able to participate in this thread. 
I'm still learning this stuff, so bear with me.
I feel we need to take a deeper look into our raw data and start collecting SNP's that may be of interest to CFS, POTS and any other chronic illnesses we all suffer from. I hope to continue adding to this list. I will try to keep this post edited with all of the important SNP's mentioned. If you could please keep the Dr Amy Yasko methylation SNP's out of this thread, I'd appreciate it. There are many threads on this topic and I wanted to explore new areas.
*Get SNPtips for Firefox
If you have not done so yet, I highly recommend installing a Firefox addon called SNPtips that will make checking your genotypes a lot easier while browsing the web. With this addon installed, all RS Id's will become clickable and will allow you to see your genotype without having to even visit the 23andme website. This thread will be written as if you have SNPtips installed. I'm not going to be directly linking back to 23andme when there's an addon that does it for you. Sorry. Even if you don't use firefox usually, I recommend downloading it and using it while looking at genetic information.
*Recommended 3rd Party Tools
There is a website that lists a bunch of 3rd party tools you can use to get more information out of your data. You can find that here.
http://www.23andyou.com/3rdparty
Promethease-Highly recommended http://snpedia.com/index.php/Promethease This program will run your raw data through their system and flag specific SNP's that have been studied to increase your risk for diseases or seen more often in certain conditions etc. It is going to find things that 23andme does not report on. I found out some amazing stuff with this tool. If you have run your data through Promethease and found something interesting, please post the related RS Id's with a brief description, so we can all take a look. I will keep this post edited (as often as I can) with all of the SNP's mentioned.
Interpretome-Very similar to Promethease. http://esquilax.stanford.edu/ It will give you data based upon your genotypes on specific SNPs.
ROH and No Call Strings Check-http://www.math.mun.ca/~dapike/23roh.php This utiltity will look at your raw data and see how much homozygosity is in your genetics. Typically one would call this "how inbred" you are... It will also check for No Call strings which may indicate a mutation or microdeletion. I can't offer detailed support with this tool as I am learning it on my own, but I can give general ideas of what the data means. Please see this 23andme thread for more information. https://www.23andme.com/you/community/thread/3093/
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* APOE Status
APOE E4 is considered the bad one. It has been implicated in alzheimer's. Those with the genetic allele ApoE4 protein in the blood have been found to detoxify metals poorly and to be much more genetically susceptible to chronic neurological conditions than those with types ApoE2 or E3 Source
23andme files this under the Alzheimer's health report. This one is determined by 2 SNP's and it can be a little confusing, so I recommend taking a look at the report.
https://www.23andme.com/you/journal/alzheimers/overview/
If you have data from another company, then these are the 2 Rs Id's associated with it. It is more difficult to determine than a simple TT or CC.
If you are CT at rs429358 and CC at rs7412 you would be e3/e4.
If you are TT at rs429358 and CC at rs7412 you would be e3/e3. This is most common.
If you are CC or CT at rs429358 and CT at rs7412 you would be e2/e4 or the rare e3r. This combo is rare and not well understood. See this study.
If you are CC at rs429358 and CC at rs7412 you would be e4/e4.
If you are TT at rs429358 and CT at rs7412 you would be e2/e3.
This should cover all possible variations. CC at rs429358 and TT at rs7412 has never been seen according to 23andme.
*Liver Pathways
With liver pathways, there are a ton of SNP's, so only a few of them are listed here.
CYP1A2 is one of the main liver pathways which metabolizes caffeine, estrogen, naproxen, propranolol, acetaminophen and many many more drugs. Here's a link to more data about this from mayo clinic.
CYP1A2 rs762551 Each C is a copy of slower function.
Therefore AA=normal; AC=intermediate ; CC=slow metabolism
23andme has a report on this here. https://www.23andme.com/you/journal/pre_caffeine_metabolism/overview/
More SNPs related to CYP1A2 are listed here at SNPedia. http://www.snpedia.com/index.php/CYP1A2
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CYP2C9 is another liver pathway which metabolizes Warfarin, NSAID's, aspirin, phenytoin and more. Here's a link to data from Mayo Clinic.
CYP2C9*2 rs1799853 Each T is a copy of slower function.
Therefore CC=normal; CT=intermediate TT=Slow
CYP2C9*3 rs1057910 Each C is a copy of slower function.
Therefore TT=Normal; CT=Intermediate CC=Slow
More SNP's related to CYP2C9 are listed here at SNPedia. http://www.snpedia.com/index.php/CYP2C9
_____________________________________________________________________________________________________________
CYP2D6(Directly from SNPedia) Almost 25% of all drugs are metabolized by CYP2D6, including dextromethorphan (a key ingredient in products such as Nyquil), beta-blockers, antiarrhythmics, and antidepressants.
This one is not easily decided by a single SNP, so I looked at the genoset 182 at SNPedia to determine this. I'm not entirely sure how this one is determine. I highly recommend seeing what Promethease has to say about your result specifically.
rs1135840 G=risk allele for rapid metabolism
rs16947 A=risk allele for rapid metabolism
A word of caution from SNPedia, "Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. "
_____________________________________________________________________________________________________________
NAT2 (Directly from SNPedia) N-acetyltransferases are enzymes acting primarily in the liver to detoxify a large number of chemicals, including caffeine and several prescribed drugs. The NAT2 acetylation polymorphism is important because of its primary role in the activation and/or deactivation of many chemicals in the body's environment, including those produced by cigarettes as well as aromatic amine and hydrazine drugs used medicinally.
Interpreting the alleles for this is more confusing. Check out this website and input your genotypes to find out whether you are rapid, intermediate or slow.
These are the SNP's and corresponding positions, so you know what to input.
NAT2 sequence position with RS ID's
282 =Rs1041983
341= Rs1801280
481= Rs1799929
590= Rs1799930
803= Rs1208
857= Rs1799931
Preliminary data suggests Rs1495741 accurately predicts NAT2 metabolism. Each copy of A suggests slow metabolism.
Therefore GG=Rapid; AG=Intermediate; AA=Slow
In this thread, LaurieL posted a study that found rapid NAT2 and CYP2D6 metabolism was seen more often in those with Multiple chemical sensitivity than in controls.
For more information on this pathway see SNPedia http://www.snpedia.com/index.php/NAT2 and Promethease.
__________________________________________________________________________________________________________________________________
VKORC1 is related to Warfarin metabolism and vitamin K recycling.
Rs9923231 For each T=increased sensitivity to Warfarin. This genotype frequency is highly varied among different populations.
For more information on drug metabolism and liver pathways see the article on SNPedia. There are many more I did not list here.
________________________________________________________________________________________________________
*Celiac Disease
Rs2187668= For each T, increases risk. This is testing for HLA-DRB1*0301 or the DQ2.5 Haplotype. This SNP is also associated with other autoimmune disorders.
rs6822844= For each G, increases risk.
rs6441961= For each T, increases risk.
Rs2074404=GG Seen in higher rate in those with Celiac
_________________________________________________________________________________________________________________
Sections I'd like to add in the future after more research:
Autoimmune SNP's for lupus, sjorgren's etc.
Collagen SNP's for connective tissues disorders and EDS
HLA data if this can be figured out... Many people online are still trying to do this. It is not available yet.
Give me some ideas/suggestions...
I'm still learning this stuff, so bear with me.I feel we need to take a deeper look into our raw data and start collecting SNP's that may be of interest to CFS, POTS and any other chronic illnesses we all suffer from. I hope to continue adding to this list. I will try to keep this post edited with all of the important SNP's mentioned. If you could please keep the Dr Amy Yasko methylation SNP's out of this thread, I'd appreciate it. There are many threads on this topic and I wanted to explore new areas.
*Get SNPtips for Firefox
If you have not done so yet, I highly recommend installing a Firefox addon called SNPtips that will make checking your genotypes a lot easier while browsing the web. With this addon installed, all RS Id's will become clickable and will allow you to see your genotype without having to even visit the 23andme website. This thread will be written as if you have SNPtips installed. I'm not going to be directly linking back to 23andme when there's an addon that does it for you. Sorry. Even if you don't use firefox usually, I recommend downloading it and using it while looking at genetic information.
*Recommended 3rd Party Tools
There is a website that lists a bunch of 3rd party tools you can use to get more information out of your data. You can find that here.
http://www.23andyou.com/3rdparty
Promethease-Highly recommended http://snpedia.com/index.php/Promethease This program will run your raw data through their system and flag specific SNP's that have been studied to increase your risk for diseases or seen more often in certain conditions etc. It is going to find things that 23andme does not report on. I found out some amazing stuff with this tool. If you have run your data through Promethease and found something interesting, please post the related RS Id's with a brief description, so we can all take a look. I will keep this post edited (as often as I can) with all of the SNP's mentioned.
Interpretome-Very similar to Promethease. http://esquilax.stanford.edu/ It will give you data based upon your genotypes on specific SNPs.
ROH and No Call Strings Check-http://www.math.mun.ca/~dapike/23roh.php This utiltity will look at your raw data and see how much homozygosity is in your genetics. Typically one would call this "how inbred" you are... It will also check for No Call strings which may indicate a mutation or microdeletion. I can't offer detailed support with this tool as I am learning it on my own, but I can give general ideas of what the data means. Please see this 23andme thread for more information. https://www.23andme.com/you/community/thread/3093/
* APOE Status
APOE E4 is considered the bad one. It has been implicated in alzheimer's. Those with the genetic allele ApoE4 protein in the blood have been found to detoxify metals poorly and to be much more genetically susceptible to chronic neurological conditions than those with types ApoE2 or E3 Source
23andme files this under the Alzheimer's health report. This one is determined by 2 SNP's and it can be a little confusing, so I recommend taking a look at the report.
https://www.23andme.com/you/journal/alzheimers/overview/
If you have data from another company, then these are the 2 Rs Id's associated with it. It is more difficult to determine than a simple TT or CC.
| APOE | Rs429358 | Rs7412 |
| e2 | T | T |
| e3 | T | C |
| e4 | C | C |
If you are CT at rs429358 and CC at rs7412 you would be e3/e4.
If you are TT at rs429358 and CC at rs7412 you would be e3/e3. This is most common.
If you are CC or CT at rs429358 and CT at rs7412 you would be e2/e4 or the rare e3r. This combo is rare and not well understood. See this study.
If you are CC at rs429358 and CC at rs7412 you would be e4/e4.
If you are TT at rs429358 and CT at rs7412 you would be e2/e3.
This should cover all possible variations. CC at rs429358 and TT at rs7412 has never been seen according to 23andme.
*Liver Pathways
With liver pathways, there are a ton of SNP's, so only a few of them are listed here.
CYP1A2 is one of the main liver pathways which metabolizes caffeine, estrogen, naproxen, propranolol, acetaminophen and many many more drugs. Here's a link to more data about this from mayo clinic.
CYP1A2 rs762551 Each C is a copy of slower function.
Therefore AA=normal; AC=intermediate ; CC=slow metabolism
23andme has a report on this here. https://www.23andme.com/you/journal/pre_caffeine_metabolism/overview/
More SNPs related to CYP1A2 are listed here at SNPedia. http://www.snpedia.com/index.php/CYP1A2
_______________________________________________________________________________________________________________
CYP2C9 is another liver pathway which metabolizes Warfarin, NSAID's, aspirin, phenytoin and more. Here's a link to data from Mayo Clinic.
CYP2C9*2 rs1799853 Each T is a copy of slower function.
Therefore CC=normal; CT=intermediate TT=Slow
CYP2C9*3 rs1057910 Each C is a copy of slower function.
Therefore TT=Normal; CT=Intermediate CC=Slow
More SNP's related to CYP2C9 are listed here at SNPedia. http://www.snpedia.com/index.php/CYP2C9
_____________________________________________________________________________________________________________
CYP2D6(Directly from SNPedia) Almost 25% of all drugs are metabolized by CYP2D6, including dextromethorphan (a key ingredient in products such as Nyquil), beta-blockers, antiarrhythmics, and antidepressants.
This one is not easily decided by a single SNP, so I looked at the genoset 182 at SNPedia to determine this. I'm not entirely sure how this one is determine. I highly recommend seeing what Promethease has to say about your result specifically.
rs1135840 G=risk allele for rapid metabolism
rs16947 A=risk allele for rapid metabolism
A word of caution from SNPedia, "Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. "
_____________________________________________________________________________________________________________
NAT2 (Directly from SNPedia) N-acetyltransferases are enzymes acting primarily in the liver to detoxify a large number of chemicals, including caffeine and several prescribed drugs. The NAT2 acetylation polymorphism is important because of its primary role in the activation and/or deactivation of many chemicals in the body's environment, including those produced by cigarettes as well as aromatic amine and hydrazine drugs used medicinally.
Interpreting the alleles for this is more confusing. Check out this website and input your genotypes to find out whether you are rapid, intermediate or slow.
These are the SNP's and corresponding positions, so you know what to input.
NAT2 sequence position with RS ID's
282 =Rs1041983
341= Rs1801280
481= Rs1799929
590= Rs1799930
803= Rs1208
857= Rs1799931
Preliminary data suggests Rs1495741 accurately predicts NAT2 metabolism. Each copy of A suggests slow metabolism.
Therefore GG=Rapid; AG=Intermediate; AA=Slow
In this thread, LaurieL posted a study that found rapid NAT2 and CYP2D6 metabolism was seen more often in those with Multiple chemical sensitivity than in controls.
For more information on this pathway see SNPedia http://www.snpedia.com/index.php/NAT2 and Promethease.
__________________________________________________________________________________________________________________________________
VKORC1 is related to Warfarin metabolism and vitamin K recycling.
Rs9923231 For each T=increased sensitivity to Warfarin. This genotype frequency is highly varied among different populations.
For more information on drug metabolism and liver pathways see the article on SNPedia. There are many more I did not list here.
________________________________________________________________________________________________________
*Celiac Disease
Rs2187668= For each T, increases risk. This is testing for HLA-DRB1*0301 or the DQ2.5 Haplotype. This SNP is also associated with other autoimmune disorders.
rs6822844= For each G, increases risk.
rs6441961= For each T, increases risk.
Rs2074404=GG Seen in higher rate in those with Celiac
_________________________________________________________________________________________________________________
Sections I'd like to add in the future after more research:
Autoimmune SNP's for lupus, sjorgren's etc.
Collagen SNP's for connective tissues disorders and EDS
HLA data if this can be figured out... Many people online are still trying to do this. It is not available yet.
Give me some ideas/suggestions...
