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Rare allele data

Discussion in 'Genetic Testing and SNPs' started by Valentijn, Jun 28, 2013.

  1. roxie60

    roxie60 Senior Member

    Central Illinois, USA
    I wondered that also since I found another SNP in SNPedia that I do not have the risk alelle for and it is realted to the one I do so left me wondering if you need multiple similar bad ones to have an issue. It is all so complex.
  2. roxie60

    roxie60 Senior Member

    Central Illinois, USA
    I wondered why he would blame white spots on something I only get 4-5 times a year (I feel so bad for those who have to deal with migraines more frequently, they are so debilitating). Still doesnt make sense to me so makes me suspect he just doesnt know why I had white spots.
  3. frenchmoxie


    Chrom 1

    rs4373782 CT
    rs17366686 AC
    rs28384834 AG
    rs12142450 AG

    Chrom 2

    rs45471294 CT
    rs17648863 CC
    rs11695913 CT

    Chrom 3

    rs34911341 CT
    rs1800146 GT
    rs34166957 AG
    rs13096071 CT

    Chrom 4

    rs17626658 CT
    rs10446841 GG

    Chrom 5

    rs17435258 GT
    rs13161296 CT
    rs245071 CT
    rs3213102 CT

    Chrom 6

    rs34500563 AG
    rs12202093 CT

    Chrom 7

    rs28381714 CT
    rs17876184 AG

    Chrom 8

    rs35909721 AG
    rs17736439 AG
    rs13252585 AC

    Chrom 9

    rs10972206 AG

    Chrom 10

    rs11188150 AG

    Chrom 11

    rs326221 CT

    Chrom 12

    rs61688134 CT
    rs17528736 CT
    rs35075600 CT
    rs28360457 AG

    Chrom 13

    rs17080230 AG
    rs9516949 AG

    Chrom 14

    rs11499034 CC SEL1L

    Chrom 15

    rs2304341 CT
    rs12910678 CT
    rs34261044 AG
    rs8042511 AC

    Chrom 16

    rs1800725 AG
    rs8176928 GG DNASE1
    rs1152084 CT

    Chrom 17

    rs60831116 GT
    rs2727338 AG
    rs2678672 AG FAM100B

    Chrom 19

    rs34442879 CT BCKDHA - maple syrup urine disease
    rs28399656 AT BCAM
    rs3218772 CT

    Chrom 20

    rs3176126 AG intergenic

    X chrom

    rs2773 AG USP9X
    Valentijn likes this.
  4. bel canto

    bel canto Senior Member

    Hey, frenchmoxie - thx for posting those. Those of us who have the SNPTips add-on to Firefox can see our own alleles whenever we see the rs #'s. However, if the letters are right next to the rs# (rs444444TT), it doesn't work. With a space (rs444444 TT), it does.
    Can you modify your post to add the spaces? That way we can see whether we share any of these.
    frenchmoxie likes this.
  5. Valentijn

    Valentijn Senior Member

    Yes please - could you send it via private message? :D
  6. GypsyA


    Hi Valentijn!

    My personal 23andme results are in. I already shared my daughter's info with you and have been learning from everyone about what's going on with my daughter's genes. Now it's time to review mine! :) However, my brain is kind of on a bit of a vacation the past few days. So, I need a reminder, please...

    I ran my 23andme data through the Genetic Genie. There was a rare allele program I used for my daughter, but now I don't know where I found that. :-/ Can you, or someone here, remind me where to go to get the rare allele data?

    Valentijn likes this.
  7. Valentijn

    Valentijn Senior Member

    http://sourceforge.net/projects/analyzemygenes/ is a new one me and my fiance have made, which is a download - hence much much faster than the other sites. The instructions and additional information are at http://sourceforge.net/p/analyzemygenes/wiki/Home/

    This is the other one if you want to use it instead, which requires a lot of cutting and pasting: http://www.ianlogan.co.uk/23andme/minor_allele_data.htm
    GypsyA and ukxmrv like this.
  8. leela

    leela Slow But Hopeful

    Couchland, USA
    I am having trouble understanding, since SNPedia doesn't have most of them, though diseasome was a little helpful.
    So....help from Valentijn please, if you're up for it?

    Still and all, cool program, @Valentijn!

    ETA: the pdf is not loading. oops.
    Last edited: Oct 31, 2013
    Valentijn likes this.
  9. Valentijn

    Valentijn Senior Member

    These are just a list of very rare SNPs which some ME/CFS patients have in common. There might not be info available for many of them. Though currently I'm comparing bigger lists of homozygous mutations, which are more likely to have an impact.

    Which pdf are you referring to?
  10. leela

    leela Slow But Hopeful

    Couchland, USA
    Sorry, @Valentijn very brainfogged today, should probably refrain from posting!
    I meant the pdf of my rare alleles report from your sourceforge.
  11. SickOfSickness

    SickOfSickness Senior Member

    Is there a new thread for this? I see it hasn't been updated.

    I ran the 10% database and I looked for all red or orange SNPs in post #42. I have only 1.

    rs1799931...NAT2 which @ukxmrv has

    My data is not complete because I have an old 23andme chip.

    They know a lot about NAT2:
    If I am reading it correctly, I did not read a lot: this SNP explains why I am a rapid metabolizer, which is a good thing. You don't want to be a slow metabolizer.
    roxie60 and ukxmrv like this.
  12. GypsyA


    @Valentijn , I received notice that your program had an update. Do you want me to resend my results?


  13. Valentijn

    Valentijn Senior Member

    Nah, no need! The updates have all been for functionality (mostly on Macs), and don't impact on the results.
    ukxmrv and merylg like this.
  14. Tunguska

    Tunguska Senior Member

    Well this has been interesting. Thank you for this program.

    How many results (snps/lines) have people gotten on average? I got exactly 100. Only one homozygous (rs13229564) but no info about it.

    Interesting findings for me were two heterozygous, rs9332239 (CYP2C9) and rs28365083 (CYP3A5), involved in the processing of certain medications, including NSAIDs and others. Because it just so happens I've had serious reactions involving such medications recently.
    Valentijn likes this.
  15. Valentijn

    Valentijn Senior Member

    I think 100 is pretty average. Some have more, some less. And it also depends on the chip used by 23andMe when your results were processed. It's made to work with the prior chip, and tends to pick up far fewer SNPs on the new one (60 or less).

    Your homozygous result does look like a very boring one! Anything starting with "i" instead of "rs" is usually far more interesting, and will have the rs number listed in the final column for easier researching.

    The rarest SNPs can also be interesting, even when heterozygous. Usually a fair few of those are missense mutations, which can have much bigger impacts.
  16. Tunguska

    Tunguska Senior Member

    It was the new chip. I read them over again and I'm not sure my rare hetero SNPs I wrote above actually have any impact on their genes or would be missense, but interesting nonetheless.

    I ran my results through the 10% database too and filtered for the homozygous; got 670 homo; looked them up to find 16 documented. Much more interesting ones there, involving correlations with retinal detachment and keratoconus, yikes. Not much CFS-related except some immunity-related one.

    Anyway, just realized I posted my comment in the wrong thread, sorry.

    (Oh and turns out I DID have a fatigue-related one which I've made another thread for, but it was 2% not 1% so the first pass didn't catch it)
    Last edited: Jun 2, 2014
  17. MegHurley36


    Here is my report, I have no idea how it correlates, but if anyone does know, reply here???

    PS I was told years ago have chronic fatigue, chronic mono, Epstein barr, and lyme.... but I was just tested and have mito dys and metabolic syndrome from a reaction to fluoquinolones. I have healed a ton, but still need more info of course :) Still def in lots of minerals and vitamins, still horribly fatigued, and rashing all the time.

    Wonder what was 'triggered'


    rs12116440 1 T 1.00 CT
    rs3918018 1 T 1.00 CT
    rs16846495 1 T 0.23 CT
    rs35814900 1 A 1.00 AG
    rs2232363 1 A 1.00 AG
    rs11120537 1 C 1.00 AC
    rs72466494 2 T 0.41 CT
    rs12185694 2 T 1.00 GT
    rs12619170 2 C 0.00 AC
    rs10496708 2 T 1.00 CT
    rs13400424 2 A 1.00 AG
    rs17205728 2 T 1.00 CT
    rs13012441 2 G 1.00 AG
    rs12993807 2 A 1.00 AG
    rs4494742 2 T 1.00 CT
    rs3731062 3 A 1.00 AG
    rs17201603 3 A 1.00 AG
    rs10935179 3 T 1.00 GT
    rs13098532 3 G 1.00 GT
    rs292050 4 T 1.00 GT
    rs1605208 4 G 1.00 AG
    rs11573780 4 T 1.00 CT
    rs11249470 4 G 1.00 AG
    rs283410 4 A 1.00 AG
    rs6816876 4 G 1.00 AG
    rs12374404 4 T 1.00 CT
    rs17402629 4 A 1.00 AG
    rs4505907 5 C 1.00 CT
    rs35629723 5 G 0.37 CG
    rs36105360 5 T 1.00 CT
    rs61754582 5 A 1.00 AG
    rs6884056 5 C 1.00 CT
    rs3213102 5 T 1.00 CT
    rs17876047 5 A 1.00 AG
    rs28404158 5 C 1.00 AC
    rs11575840 6 T 1.00 CT
    rs2234080 6 A 1.00 AG
    rs17453041 6 G 1.00 AG
    rs1424935 6 G 1.00 AG
    rs34130495 6 A 1.00 AG
    rs35956182 6 A 0.46 AG
    rs28405775 7 A 1.00 AG
    rs7799716 7 G 1.00 AG
    rs1990554 7 A 1.00 AC
    rs13232752 7 A 1.00 AG
    rs12534162 7 G 1.00 AG
    rs72555745 7 C 1.00 CT
    rs6970680 7 A 1.00 AG
    rs17290246 7 A 1.00 AG
    rs41279857 7 T 0.09 GT
    rs176479 7 C 1.00 CT
    rs6471672 8 G 1.00 AG
    rs2513812 8 G 1.00 GT
    i5007196 8 G 0.23 AG rs121908601
    rs2993177 9 A 1.00 AG
    rs13286453 9 T 1.00 CT
    rs17211882 9 A 1.00 AG
    rs11243406 9 A 1.00 AC
    rs2457838 10 G 1.00 GT
    rs1943 10 T 1.00 CT
    rs11598891 10 T 1.00 CT
    i5009017 10 A 0.05 AG rs116040871
    rs17805341 10 T 1.00 GT
    rs10894690 11 C 1.00 CT
    rs17722134 12 G 1.00 AG
    rs17220870 13 T 1.00 CT
    rs10507683 13 T 1.00 CT
    rs17619183 13 C 1.00 AC
    rs17458021 15 T 1.00 GT
    rs611704 16 A 1.00 AG
    rs12918121 16 T 1.00 CT
    rs2090019 17 T 1.00 CT
    rs17590785 17 A 1.00 AG
    rs2016648 17 T 1.00 CT
    rs12962762 18 T 1.00 CT
    rs4987817 18 A 1.00 AG
    rs17181586 18 A 1.00 AG
    rs1538012 19 A 1.00 AG
    rs193234 19 G 1.00 GT
    rs11671231 19 T 1.00 CT
    rs17327630 20 A 1.00 AC
    rs709046 20 T 1.00 CT
    rs17219643 20 T 1.00 CT
    rs139740 22 A 1.00 AG
    rs5752023 22 T 1.00 GT
    rs1046166 22 T 0.37 CT
    rs139275 22 A 1.00 AG
    rs4253791 22 A 1.00 AT
    rs11796544 X A 1.00 AG
    rs5952669 X T 1.00 CT
    rs5905625 X G 1.00 AG
    rs2207084 X A 1.00 AG
    rs10521360 X C 1.00 CT
    rs12559201 X T 1.00 CT
    rs17317849 X C 1.00 CT
  18. August59

    August59 Daughters High School Graduation

    Upstate SC, USA
    What program is being used to "unzip" the downloaded file. The following instructions don't seem follow WinZip or Win Rar?

    6) Go to the folder where you extracted the files
    7) Double-click on the "Genes"
    8) A grey box with three buttons appears. The top one should be green. If it isn't, click on it to navigate to whatever dodgy location you've put the "one_percent" file in.
    9) Click on the orange middle box to select your 23andMe file.
    10) Click the yellow "Analyze" button, and wait for it to finish. This takes 52 seconds on my newish but basic laptop.

  19. Valentijn

    Valentijn Senior Member

    @MegHurley36 - I'll take a quick look. Mostly I use dbSNP to see if there's anything interesting. Would you prefer I post here if I see anything of interest, or that I send you a private message via the forum Conversation function?
  20. MegHurley36


    @Valentijn Here would be fabulous I think If it is anything truly horrible you can msg me lol. No, I like to contribute where I can. :)
    Sorry if I am slow in responding, brain fog has been higher than norm. I accidentally took 5gm of folinic acid 2 days ago. Interesting, that my rash is now clearing, yet I feel terrible. Anyhow, thank you.
    Valentijn likes this.

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