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Rare allele data

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

  1. Graham

    Graham Senior Moment

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    Hi Valentijn. Suddenly my brain feels very inadequate! I must admit that I know very little about the biology here. But I can comment on the probabilities. They are slippery little devils to deal with.

    First of all, as you suggested, if they are inherited in a clump, then you cannot treat them as though they are independent probabilities. Blond hair and blue eyes spring to mind as an example. They tend to occur together.

    Now this is where I am guessing about the biology, so if I misunderstand, please excuse me. If one minor allele has a 1% occurrence, then the odds of a person picked at random having that is 1 in 100. The probability that you and me both have that specific minor allele would be 1 in 10,000. But if you discover that I have a specific minor allele, then the probability that you have it too is 1 in 100. If you have a list of 5 people, then the chance that someone in the list besides me has it drops to 1 in 20.

    The second problem is that of picking "coincidences" in a group. The chance of two people picked at random having a shared birthday is 1 in 365 (ignoring leap years), but in a class of 30 I believe the chance of finding two people with a birthday in common is over a half. This is closer to what you are doing with your lists: you are looking for pairs with common features.

    So when you say "what are the chances that Sea and Valentijn both have ..." you can't just multiply the probabilities together. First of all I guess it is almost certain that both of them will have a number of rare alleles. Then if you pick one of Sea's, and look for a match somewhere that is not the same as calculating the probability that, picked at random, they both share one particular rare allele. If you start by looking for two people in a group that share a rare allele (like shared birthdays), it would be very very time consuming to calculate the odds. What you can say is that if several people share that rare allele, then that would be against the odds.

    I have a similar personal gripe when my wife complains to the GP about a side effect of blood pressure medication, and is told that it can't be because the odds are 10,000 to 1 against. It is the wrong probability. Suppose the very rare side effect is to produce a nose that glows in the dark. If, after taking the medication, her nose starts to glow in the dark then we are no longer dealing with theoretical probabilities (a priori). Instead we now need to know, given that she is taking the medication, what is the probability of it being the medication in comparison with all of the other probabilities? (and that is very different). These are conditional probabilities.

    I think I have got that straight, and I hope it is useful. Certainly the data that you have found is potentially very interesting, I'd just be wary of working out the odds. Now to rest my brain. I'll go and open up the greenhouse.
    Sea and Valentijn like this.
  2. Valentijn

    Valentijn Activity Level: 3

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    Thanks, I think you answered my questions ... I wasn't so sure about the dividing by the (remaining?) group size (especially when we have 3 full sets of results and two results for single SNPs :confused:). I'll try to rework the numbers and see if I can do better!
  3. Valentijn

    Valentijn Activity Level: 3

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    Okay, here's the corrected odds (hopefully!):

    rs10036862 (??)
    1.0% prevelance of the minor allele. 1 in 100 people have it. The probability that a 2nd person in a group of 3 would have it is 1 in 50 (Graham - we have 3 full sets of results, 1 is the "original" result, leaving 2 that might or might not have it, hence dividing by 2?).

    rs1407268 (??)
    1.0% prevelance of the minor allele. 1 in 100 people have it. The probability that a 2nd person in a group of 3 would have it is 1 in 50.

    rs12751479 (DPYD)
    0.1% prevalence of the minor allele. 1 in 1,000 people have it. The probability that a 2nd person in a group of 3 would have it is 1 in 500.

    rs1699499 (FANCC)
    1.0% prevelance of the minor allele. 1 in 100 people have it. The probability that a 2nd person in a group of 3 would have it is 1 in 50.

    rs34409923 (FER1L5)
    0.8% prevalance of the minor allele. 1 in 125 people have it. The probability that two random people have that same allele is 1 in 63.

    rs306781 (GSN)
    1.0% prevelance of the minor allele. 1 in 100 people have it. The probability that a 2nd person in a group of 3 would have it is 1 in 50.

    rs17526980 (KIF13B)
    0.7% prevalence of the minor allele. 1 in 143 people have it. The probability that someone with one allele also has the 2nd allele is 1 in 143, and that a 2nd person in a group of 3 has one allele is 1 in 10,225 (1/143 * 2/143 - Graham? :))


    rs11568438 (SLC7A7)
    0.7% prevalence of the minor allele. 1 in 143 people have it. The probability that a 2nd person in a group of 3 would have it is 1 in 72.

    So what are the odds that Sea and Valentijn both have minor alleles for rs10036862 (??), rs1407268 (??), and rs306781 (GSN)? Two of those (rs10036862 and rs1407268) have exactly the same prevalance in various groups, so are probably inherited as a clump - thus everyone with a minor allele in one has a minor allele in the other, and only one result is relevant. But the probability that Sea would both have that minor allele and the GSN minor allele the same as Valentijn is 1 in 2500.

    And what are the odds that Sea and nandixon both have minor alleles for rs12751479 (DPYD), rs1699499 (FANCC), rs34409923 (FER1L5), and rs11568438 (SLC7A7)? These all look like unrelated SNPs, so each result is probably relevant. The probability that nandixon would have 4 of the same minor alleles as Sea is 1 in 113,400,00.

    So that's still some rather significant results, especially for the multiple alleles shared by Sea and nandixon.
  4. Graham

    Graham Senior Moment

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    Hi Valentijn. Nearly there now, but the difficulty is that the correct answer depends very precisely upon what you are considering. This is where my knowledge of biology breaks down (last studied when I was 12!).

    So suppose we have three people, Alex, Billy and Cass. There are four characteristics, A, B, C and D, with variations A1 (prob 0.01), B1 (0.02), C1 (0.001) and D (0.01). There are 16 different possible sets of results (such as A, B, C1, D).

    (a) So what is the probability that Alex and Billy will have at least one variation in common?
    0.01 x 0.01 + 0.02 x 0.02 + 0.001 x 0.001 + 0.01 x 0.01 = 0.0006 (rounded off)

    (b) The probability that Alex and Billy, or Alex and Cass, or Billy and Cass have at least one variation in common is
    0.0006 x 3 = 0.0018 (about 1 in 556)

    (c) But if you know that Alex has A, B1, C, and D1 the chance that Billy has a variation in common is 0.02 (for B) + 0.01 (for D) = 0.03. The fact that this is so much bigger that (a) seems at odds with common sense, but of course there is only a tiny chance that Alex has any of the variations in my example, so knowing that he does changes the odds considerably.

    The odds of someone not having any of these variations is 0.99 x 0.98 x 0.999 x 0.99 = 0.96 (rounded to 2 dp), so only 4 in 100 would have the variations. I'm guessing that the odds of anyone being free from minor alleles in your analysis is pretty tiny, but you would have to carry out a pretty long calculation on every single one. I'm guessing that the difference between (a) and (c) would be very much less in reality (unless Alex's results or Billy's results were unusual: say one had more variations than normal).

    Now we get onto deep philosophy. When you toss a coin, we all say that the odds of it being heads or tails is 50:50. Well that could be the case before you toss it, but once it is tossed, even before you see it, it is either a head or a tail. There is no probability about it. There is a probability of you guessing it correctly though.

    So if Billy has A, B1, C, D and E1, there is no probability associated with Billy having a variation in common with Alex. He already does, B1. What we actually talk about is the expectation that this would happen. The answer to that is whether you are asking what is the expectation that they both have B1 in common (0.01 x 0.01=0.0001), whether they both have one or more variations in common (0.0006 from (a)), or, knowing that Alex has B1 and D1, what are the odds that Billy has B1 or D1 or both (0.02 + 0.01 = 0.03).

    I'm guessing that two people having the same minor allel in common is not that noteworthy.

    The next step up is to work out the expectation that two people could have two variations in common. Now you have the chance that they both have A1 and B1 (0.01 x 0.01) x (0.02 x 0.02) x(1 - 0.001 x 0.001) x (1 - 0.01 x 0.01) plus the chance that they have A1 and C1 ....

    Are you sure that you really want to go through with this? I'm getting foggy, so I hope that I have got it right, but am not convinced.

    Personally I've lost the will to live, so am going into the garden to close up the greenhouse.
    Valentijn likes this.
  5. Graham

    Graham Senior Moment

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    Sorry about going into teacher mode. It's a hard habit to break.
  6. Valentijn

    Valentijn Activity Level: 3

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    Nah, it's what I wanted :) A comprehensible and thorough explanation. And I think I actually understood it all - after reading it for a 2nd time after a good night's sleep :D

    The rare results we're showing are coming from a list of over 22,000 rare SNPs (960,000 SNPs tested in total). So I'm sure that list size affects the odds (but not probabilities?) of getting shared results. Albeit in a complicated matter which probably doesn't have a big impact on the results, since we're each getting 50-55 rare alleles out of a much bigger sample.
  7. Valentijn

    Valentijn Activity Level: 3

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    Here's the table, now updated with ukxmrv's full results included:

    RSID.......GENE........MA.VAL.UKX.MER.SEA.NAN
    rs10036862..??..........A..AG..........AG
    rs10840932..??..........C......CT
    rs11199654..??..........A..............AG
    rs11673485..??..........T..............GT
    rs11765511..??..........T..CT
    rs11967812..??..........C..............CT
    rs12094954..??..........T..................CT
    rs12189802..??..........T..............CT
    rs12202093..??..........C..CT
    rs12554509..??..........T......CT
    rs12845411..??..........T..CT
    rs13006003..??..........A......AG
    rs13071214..??..........C..............CT
    rs13096071..??..........C..................CT
    rs1364778...??..........A..AG
    rs1407268...??..........G..AG..........AG
    rs17193729..??..........G..............AG
    rs17208220..??..........T......CT......CT
    rs17322331..??..........T.. ...............CT
    rs17473279..??..........G..................AG
    rs17581686..??..........T..................CT
    rs17632157..??..........T..............CT
    rs17786289..??..........A..............AG
    rs220378....??..........C..................AC
    rs2301187...??..........G..............GT
    rs2303965...??..........T..............CT
    rs2448326...??..........T..GT
    rs273466....??..........A......AG
    rs273469....??..........C......CT
    rs2812230...??..........C..................CT
    rs313273....??..........A..AG
    rs35909721..??..........A..............AG
    rs17208220..??..........T......CT
    rs6627746...??..........T..............CT
    rs7247965...??..........A..................AC
    rs8042511...??..........C..................AC
    rs12154319..ABCB1.......A..AG
    rs58843120..ABCB9.......T..................GT
    rs56131651..ABCC2.......A..AG
    rs11568605..ABCC3.......T..................CT
    rs60681475..ABCC11......T......CT
    rs3730044...ACE.........A..AG
    rs4968......ADD1........T..............CT
    rs7713754...AFF4........C..CT
    rs17349278..AJAP1.......T..............GT
    rs11239373..ANKRD30BP3..C..CT
    rs11246353..AP2A2.......A..AG
    rs34552278..AQP3........A..............AG
    rs11697265..ATP5E.......C......CT
    rs41273157..ATP13A2.....T..CT
    rs11797182..BEX1........G..AG
    rs11090143..BIK.........T......CT
    rs1799954...BRCA2.......T..............CT
    rs4988346...BRIP1.......T..................CT
    rs11055389..C12orf36....A......AG
    rs59286323..CACNA1H.....T......CT
    rs17394875..CACHD1......T..CT
    rs17679086..CASC3.......G..................AG
    rs17410855..CCD17.......T..............CT
    rs11879596..CCDC151.....A..............AG
    rs3212861...CCND1.......A......AG
    rs4135012...CDC6........A..................AG
    rs3848286...CES2........A..AG
    rs17793768..CHST12......T......CT
    rs11549260..CIZ1........T..............CT
    rs11559024..CKM.........C......CT
    rs55960271..CLCN1.......T..................CT
    rs11601245..CORO1B......T..................CT
    rs2231696...CPSF6.......G......AG
    rs4844609...CR1.........A......AA
    rs1497......CRBN........G..............GT
    rs11572144..CYP2C8......A..................AG
    rs5030656...CYP2D6......D......DI
    rs28414989..CYP4A11.....C..............CC
    rs17556220..DDX21.......T..............CT
    rs12920868..DEF8........T......CT
    rs721151....DENND4A.....A......AC
    rs8176928...DNASE1......G
    rs12751479..DPYD........T..............GT..GT
    rs12534498..DTX2........A..AG
    rs17512054..DYNC1H1.....G......AG
    rs17322140..ELF2........A..............AG
    rs8177173...EPHB6.......A..............AG
    rs2738415...ESR2........T..................CT
    rs2231855...ETV3........G..............AG
    rs17449755..EXOC6.......T..............GT
    rs5894......F2R.........G..GT
    rs2243072...F2RL1.......T......CT
    rs9332688...F5..........A..AG
    rs428199....F9..........T..CT
    rs17251337..FAAH2.......C......AC
    rs17613128..FAM134B.....T......GT
    rs11169088..FAM186B.....A..................AG
    rs11239604..FAM21C......G..AG..AG
    rs1699499...FANCC.......C..............CT..CT
    rs9658682...FAS.........G..................AG
    rs34409923..FER1L5......A..............AG..AG
    rs6054......FGB.........T......CT
    rs28384848..FMO1........C..............CT
    rs28369860..FMO2........D..............DI
    rs10495765..FOSL2.......G......AG
    rs11751917..GAPDHP72....A......AG
    rs56106312..GCNT2.......A..................AG
    rs669561....GLIS2.......T......CT
    rs11623598..GPHN........T..................CT
    rs12194562..GRM1........C..CT
    rs62638620..GRM6........A..AG
    rs306781....GSN.........C..CT..........CT
    rs3218808...GTF2H4......T..CT
    rs3218816...GTF2H4......A..AG
    rs2857533...HOXD3.......T..GT
    rs3213102...IL12B.......T..................CT
    rs1109918...IL12RB2.....G..............AG
    rs8177788...IL15RA......T..............CT
    rs1805128...KCNE1.......T..CT
    rs11227700..KDM2A.......A..................AG
    rs17526980..KIF13B......T..TT......CT
    rs11781640..KIFC2.FOXH1.T..................CT
    rs11577810..KPNA6.......T......CT
    rs35678986..KRTAP5-4....G......GT
    rs4986970...LCAT........T..................AT
    rs61737308..LINGO1......T......CT
    rs12117552..LMNA........A......AG
    rs4732359...LOC100132310A..................AG
    rs12527982..LOC100505519T..................CT
    rs11239373..LOC338579...C......CT
    rs4949212...LOC441880...G......GT
    rs17570718..MACF1.......C......AC
    rs2513812...MATN2.......G......GT
    rs3212379...MC1R........T..CT
    rs28937908..MLCYD.......C......CT
    rs1056784...MMP19.......A......AG
    rs17273542..MPDZ........A......AG
    rs17678817..MSL1........T..................CT
    rs1611772...MUC1........A..AG
    rs1799931...NAT2........A..AG
    rs1801316...NDUFA1......C..............CG
    rs60156239..NEFL........A..................AG
    rs4648039...NFKB1.......T..CT
    rs34248917..NPHP4.......T..............CT
    rs17173698..PAPSS2......A..............AG
    rs35722504..PARN........T..CT
    rs2332284...PARP9.......C..CT
    rs4151681...PCDHA?......A......AG
    rs725522....PCSK1.......A..AG
    rs1177230...PEX13.......G..................GG
    rs12195007..PHACTR1.....G..GT
    rs4135292...PPARG.......A..AG
    rs8178216...PRKDC.......A..............AG
    rs4648298...PTGS2.......C..................CT
    rs689469....PTGS2.......T..................CT
    rs17219643..PTPRT.......T..CT
    rs36074402..RAB38.......A..AG
    rs12357104..RET.........T..................CT
    rs1053360...RHD.........A..............AG
    rs17880470..PON3........G..................AG
    rs10935780..RNF13.......C..CT
    rs9976946...RUNX1.......C..............CT
    rs12144868..SCMH1.......C..............CT
    rs41276525..SCN5A.......A..............AG
    rs3917875...SELP........G..................CG
    rs1378220...SEMA6D......T......CT
    rs17284463..SEMA6D......G......AG
    rs17285093..SEMA6D......G......AG
    rs17356302..SEMA6D......G......AG
    rs17356420..SEMA6D......C......CT
    rs17356573..SEMA6D......A......AG
    rs17356726..SEMA6D......G......CG
    rs36049418..SLC12A3.....A..AG
    rs2328894...SLC17A4.....T..CT
    rs724665....SLC25A40....A..AG
    rs28914833..SLC6A4......G..AG
    rs11568438..SLC7A7......A..............AG..AG
    rs11634219..SNORD115@...A..................AG
    rs17470471..SOX6........G..............GT
    rs17648863..SPOPL.......C......CT
    rs9860312...STAC........T..CT
    rs4361233...SUSD5.......G..AG
    rs17179194..SYNE2.......A......AG
    rs2292969...TBCD........C..................CT
    rs526433....TECTA.......G..AG
    rs5029963...TNFAIP3.....G..................AG
    rs5745989...TNFRSF1B....A......AG
    rs45498900..TSC2........A......AC
    rs12884433..TSHR........T..CT
    rs12720355..TYK2........G......AG
    rs17863764..UGT1A8......G..............AG
    rs12355108..WDR11.......T..............CT
    rs17679361..WIPF2.......C..................CT
    rs34842534..XBP1........A..............AG
    rs45471294..XDH.........T..............CT
    rs12798330..ZDHHC13.....G..................AG
    rs13271123..ZFPM2.......G......AG
    rs11011379..ZNF248......C..CT
    ukxmrv likes this.
  8. nandixon

    nandixon Senior Member

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    If people find it too troublesome to manually input their 23andMe data into the program on the rare allele website that Valentijn gave in her first post, you can also upload your data on openSNP.org and the rare allele program will be run for you automatically. (The same person, Ian Logan, operates both websites; openSNP under a Massachusetts Institute of Technology license.) You do need to unzip your 23andMe data to upload it as the text file (.txt). Your rare allele results will be determined for you and a link to them provided in a message/email from Ian.
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  9. Bluebell

    Bluebell Senior Member

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    nandixon, are you sure that Ian Logan runs openSNP? The openSNP.org FAQ says, "Who is behind openSNP? The site is hosted and was coded by Bastian, Helge and Philipp." That part of their site is overwritten with layers of text and nearly unreadable (I don't know if the display problem, just in that area of their site, is due to my computer's old internet browser) but of what I can read there, I don't see a mention of Ian Logan. http://opensnp.org/faq.

    If it really is run by Ian, I'll have to change the info about that site in my methylation information list to reflect that. My prior post there is now locked from being edited, unfortunately, but I could correct it in my next iteration there.

    Do they provide a rare allele report? I did not see that offered on their site, but I must admit I just skimmed around to get a feeling of the site and didn't read in-depth. I could also add that to my description of their site, if that is correct.

    It sounds as if ("For annotation we include the manually curated SNPedia") much of their information comes from SNPedia, which itself provides the Promethease report (http://www.snpedia.com/index.php/Promethease). I am not sure if the info would be just the same, or not.

    By the way, to others reading this, the openSNP FAQ says, "you can upload the raw genotype data... The data will then be openly available for the world to see and download." "Everyone can see everything you enter and upload.... We warn every user twice about this." I would feel cautious about doing that -- but then again, I haven't run my results through any external program, even the ones that promise to keep one's data private.
    Valentijn likes this.
  10. Bluebell

    Bluebell Senior Member

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    Valenstroopwafel, I've tried all your red numbers in my 23andme raw data but I'm just boring old "normal" for all of them. :p
  11. Valentijn

    Valentijn Activity Level: 3

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    Those are just the multiple results so far. You might match up with a non-red number that another forum member has, and turn it red!

    And keep yer neanderthal mitts off my stroopwafels :cautious:
  12. nandixon

    nandixon Senior Member

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    Hi Bluebell,

    When I uploaded my 23andMe data to openSNP, a short time later I received an email from Ian Logan with a link to a publicly viewable website giving my rare allele results.
    (http://www.ianlogan.co.uk/23andme/open/nandixon.htm - just to mention here that Ian's apparently automated statement that my one homozygous result in the PEX13 gene is "unlikely to be significant as it occurs in an non-coding region" is not correct; defects in the UTR-3 can be very problematic since that portion critically affects expression of the gene...)

    You may be right, that Ian is simply associated with the website, ie, that openSNP passes along the uploaded data for him to run (automatically) in his rare allele program. I do everything from a "smart"phone and couldn't open the subsections in the FAQ when I navigated that site, and couldn't see the host names you found.

    I'm not so worried about strict privacy as perhaps some are since my CFS/ ME is quite bad and finding an effective treatment is most important to me. Discovering my PEX13 defect has been extremely helpful - it ties together all of my symptoms and lab results these past 15 years I've suffered with this illness and it provides a completely new avenue of treatment.

    I strongly recommend people pursue the rare allele analysis. You can always delete your uploaded 23andMe file from the openSNP site once you've obtained your rare allele report (that will become public of course). The more concerned can run the rare allele program manually directly from Ian's website (link in Valentijn's first post) in order to have a little more privacy.
    Valentijn likes this.
  13. Valentijn

    Valentijn Activity Level: 3

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    Ooer, that is a pretty interesting one. The gene is associated with peroxisomes, which are needed to do stuff with "very long chain fatty acids", and are involved in energy metabolism via the pentose phosphate pathway.

    Have you ever had your fatty acids or kreb's cycle substances tested? Or even cholesterol might be interesting :D
  14. Bluebell

    Bluebell Senior Member

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    I looked at a few news articles about them that openSNP has put on their "press" page, and they say that openSNP was started by a handful of German college students (none of whom are named "Ian"), so I don't think there is much information to support the idea that Ian Logan is actually behind the openSNP website, or responsible for it.

    Maybe the openSNP guys funnel people's results through Ian's program, just like they do when they match people's data with the information that is offered freely by SNPedia.

    It's kind of interesting that they would do that - piggyback on other free services - but I presume that the other services are okay with it... and more to the point, if something's freely available, it's freely available, even if a third party is doing the requesting.

    Maybe Ian Logan will work on a way to make his rare allele program easier to use, so folks don't have to publish their entire set of genetic data for the internet to see (and once there, it's always there, somewhere) simply as a way to get Ian's report done for them.

    (And I think that Valentijn and her Mr. Valentijn are working on adding a rare snp evaluation to their new analysis program.)

    I am sure that being a middleman and information broker has value in this very confusing area.

    There will be a growing need for genetic counselors who will meet with ordinary folks to discuss their genetic results and the health and lifestyle implications of them.

    Even in the Yasko area, there is a surprisingly small group of people who apparently seem to do that - at least to advertise on the internet about it (although I'm not familiar with her work and associates, so my first impressions about that program might be incorrect).

    It looks like Sterling Hill is the forerunner of people* who have monetized this kind of MTHFR analysis and advice, at least via the internet.

    There surely are others* who deal in giving advice about different areas of genetic results, of course -- like the BRCA breast cancer gene, etc.

    *By which I mean, people who are not doctors or otherwise extensively educated in biology/genetics etc., but maybe have a relevant bachelor's degree, or simply an interest and passion in the area.

    When I was researching MTHFR about a month ago, I found an extensive discussion thread on a bodybuilding forum where one of the contributors had recently become a genetic counselor about this type of thing, and he said his career has taken off massively, he's lecturing medical professionals all over the country, and he thinks the topic is poised to make a big splash in the US in the next couple of years.

    That would not be surprising, given how common the incidence of autism has become, and how common these MTHFR defects are in the general population.
  15. Bluebell

    Bluebell Senior Member

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    Ah, but I'm such a cantankerous old bird about guarding my data that I would have to do all those RS numbers by hand with 23andme, so I'll leave your non-red numbers black, and preserve some of the mystery* that pervades in the haunting bluebell woods. :cool:

    *(well, except for the TMI about BMs and stuff!)
    Valentijn likes this.
  16. Valentijn

    Valentijn Activity Level: 3

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    Well, Cragibell Bluebell, if you don't have time to both talk about your BMs and search your results for all of the rsID's listed (and I totally understand how that could happen :rolleyes: ), the ones with the minor alleles underlined and in orange are missense mutations, and typically the most relevant to dysfunctions. So if you do want to search, but much more selectively, the missense mutations are a lot more manageable.

    Or you can wait til we make a downloadable program :D
  17. Valentijn

    Valentijn Activity Level: 3

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    Updated to include the results of GypsyA's daughter (abbreviated as GyD in the last column). Red RSIDs indicate rare alleles which more than two of us have thus far. Orange minor alleles are missense or similar mutations. Homozygous results are red.


    RSID.......GENE........MA.VAL.UKX.MER.SEA.NAN.GyD
    rs10036862..??..........A..AG..........AG......AG
    rs1041926...??..........G......................AG
    rs10840932..??..........C......CT
    rs10971602..??..........T......................CT
    rs11065126..??..........A......................AG
    rs11199654..??..........A..............AG
    rs11673485..??..........T..............GT
    rs11765511..??..........T..CT
    rs11967812..??..........C..............CT
    rs12094954..??..........T..................CT
    rs12189802..??..........T..............CT
    rs12202093..??..........C..CT
    rs12554509..??..........T......CT
    rs12845411..??..........T..CT
    rs13006003..??..........A......AG
    rs13071214..??..........C..............CT
    rs13096071..??..........C..................CT..CT
    rs13232752..??..........A......................AG
    rs1364778...??..........A..AG
    rs1407268...??..........G..AG..........AG
    rs17193729..??..........G..............AG
    rs17208220..??..........T......CT......CT
    rs17322331..??..........T.. ...............CT
    rs17473279..??..........G..................AG
    rs17581686..??..........T..................CT
    rs17632157..??..........T..............CT
    rs17786289..??..........A..............AG
    rs220378....??..........C..................AC
    rs2301187...??..........G..............GT
    rs2303965...??..........T..............CT
    rs2448326...??..........T..GT
    rs273466....??..........A......AG
    rs273469....??..........C......CT
    rs2812230...??..........C..................CT
    rs313273....??..........A..AG
    rs35909721..??..........A..............AG
    rs17208220..??..........T......CT
    rs6627746...??..........T..............CT
    rs6798318...??..........G......................AG
    rs6944925...??..........A......................AC
    rs7247965...??..........A..................AC
    rs8042511...??..........C..................AC
    rs61754022..ABCA4.......T......................CT
    rs12154319..ABCB1.......A..AG
    rs11772720..ABCB5.......C......................CT
    rs58843120..ABCB9.......T..................GT
    rs56131651..ABCC2.......A..AG
    rs11568605..ABCC3.......T..................CT
    rs60681475..ABCC11......T......CT
    rs3730044...ACE.........A..AG
    rs4968......ADD1........T..............CT
    rs7713754...AFF4........C..CT
    rs34203073..AGGF1.......A......................AG
    rs34938955..AHR.........T......................CT
    rs17349278..AJAP1.......T..............GT
    rs11571365..ALOX12......T......................CT
    rs11239373..ANKRD30BP3..C..CT
    rs11246353..AP2A2.......A..AG
    rs34552278..AQP3........A..............AG
    rs11697265..ATP5E.......C......CT
    rs2231943...ATP5SL......T......................CT
    rs41273157..ATP13A2.....T..CT
    rs11797182..BEX1........G..AG
    rs11090143..BIK.........T......CT
    rs1799954...BRCA2.......T..............CT
    rs4988346...BRIP1.......T..................CT
    rs11055389..C12orf36....A......AG
    rs59286323..CACNA1H.....T......CT
    rs17394875..CACHD1......T..CT
    rs17679086..CASC3.......G..................AG
    rs17410855..CCD17.......T..............CT
    rs11879596..CCDC151.....A..............AG
    rs3212861...CCND1.......A......AG
    rs4135012...CDC6........A..................AG
    rs2582563...CEP170B.....T......................CT
    rs3848286...CES2........A..AG
    rs4778070...CHD2........A......................AG
    rs17793768..CHST12......T......CT
    rs11549260..CIZ1........T..............CT
    rs11559024..CKM.........C......CT
    rs55960271..CLCN1.......T..................CT
    rs13286360..COL27A1.....A......................AG
    rs11601245..CORO1B......T..................CT
    rs2231696...CPSF6.......G......AG
    rs4844609...CR1.........A......AA
    rs1497......CRBN........G..............GT
    rs28363488..CTNNA1......A......................AG
    rs11572144..CYP2C8......A..................AG
    rs5030656...CYP2D6......D......DI
    rs11572233..CYP2J2......A......................AG
    rs28414989..CYP4A11.....C..............CC
    rs28414989..CYP4A22.....C......................CC
    rs17556220..DDX21.......T..............CT
    rs12920868..DEF8........T......CT
    rs721151....DENND4A.....A......AC
    rs34057232..DHX16.......G......................AG
    rs17760364..DIRC1.......G......................AG
    rs12705801..DOCK4.......C......................CT
    rs8176928...DNASE1......G
    rs12751479..DPYD........T..............GT..GT
    rs12534498..DTX2........A..AG
    rs17512054..DYNC1H1.....G......AG
    rs2231801...EFS.........T......................CT
    rs17322140..ELF2........A..............AG
    rs8177173...EPHB6.......A..............AG......AG
    rs2738415...ESR2........T..................CT
    rs2231855...ETV3........G..............AG
    rs17449755..EXOC6.......T..............GT
    rs5894......F2R.........G..GT
    rs2243072...F2RL1.......T......CT
    rs9332688...F5..........A..AG
    rs428199....F9..........T..CT
    rs17251337..FAAH2.......C......AC
    rs17613128..FAM134B.....T......GT
    rs11169088..FAM186B.....A..................AG
    rs11239604..FAM21C......G..AG..AG
    rs1699499...FANCC.......C..............CT..CT
    rs9658682...FAS.........G..................AG
    rs34409923..FER1L5......A..............AG..AG
    rs6054......FGB.........T......CT
    rs28384848..FMO1........C..............CT
    rs28369860..FMO2........D..............DI
    rs10495765..FOSL2.......G......AG
    rs11751917..GAPDHP72....A......AG
    rs56106312..GCNT2.......A..................AG
    rs34116730..GCNT4.......G......................AG
    rs669561....GLIS2.......T......CT
    rs11623598..GPHN........T..................CT
    rs2235076...GRIK2.......A......................AG
    rs12194562..GRM1........C..CT
    rs2941......GRM1........A......................AG
    rs62638620..GRM6........A..AG
    rs306781....GSN.........C..CT..........CT
    rs3218808...GTF2H4......T..CT
    rs3218816...GTF2H4......A..AG
    rs2857533...HOXD3.......T..GT
    rs3213102...IL12B.......T..................CT
    rs1109918...IL12RB2.....G..............AG
    rs8177788...IL15RA......T..............CT
    rs11574627..IL2RG.......T......................CT
    rs13167382..ITK.........A......................AG
    rs13187882..ITK.........G......................AG
    rs1805128...KCNE1.......T..CT
    rs11227700..KDM2A.......A..................AG
    rs17526980..KIF13B......T..TT......CT
    rs11781640..KIFC2.FOXH1.T..................CT..CT
    rs11577810..KPNA6.......T......CT
    rs35678986..KRTAP5-4....G......GT
    rs4986970...LCAT........T..................AT
    rs61737308..LINGO1......T......CT
    rs735262....LINK00032...T......................CT
    rs12117552..LMNA........A......AG
    rs4732359...LOC100132310A..................AG
    rs12527982..LOC100505519T..................CT
    rs11239373..LOC338579...C......CT
    rs4949212...LOC441880...G......GT
    rs11564181..LRRK2.......A......................AT
    rs17570718..MACF1.......C......AC
    rs71980227..MAOA........D......................DI
    rs11756938..MAS1L.......T......................CT
    rs2513812...MATN2.......G......GT
    rs3212379...MC1R........T..CT
    rs3087450...MCM2........A......................AG
    rs17198118..MCRS1.......G......................GT
    rs28937908..MLCYD.......C......CT
    rs1056784...MMP19.......A......AG
    rs17273542..MPDZ........A......AG
    rs63750757..MSH2........A......................AG
    rs17678817..MSL1........T..................CT
    rs1611772...MUC1........A..AG
    rs1799931...NAT2........A..AG
    rs12817914..NAV3........T......................CT
    rs1801316...NDUFA1......C..............CG
    rs60156239..NEFL........A..................AG
    rs4648039...NFKB1.......T..CT
    rs11191279..NFKB2.......T......................CT
    rs34248917..NPHP4.......T..............CT
    rs10492162..OVOS........A......................AG
    rs17173698..PAPSS2......A..............AG
    rs35722504..PARN........T..CT
    rs2332284...PARP9.......C..CT
    rs4151681...PCDHA?......A......AG
    rs725522....PCSK1.......A..AG
    rs1177230...PEX13.......G..................GG
    rs12195007..PHACTR1.....G..GT
    rs4135292...PPARG.......A..AG
    rs8178216...PRKDC.......A..............AG
    rs4648298...PTGS2.......C..................CT
    rs689469....PTGS2.......T..................CT
    rs17219643..PTPRT.......T..CT
    rs36074402..RAB38.......A..AG
    rs12357104..RET.........T..................CT..CT
    rs1053360...RHD.........A..............AG
    rs11573531..POLA1.......T......................CT
    rs17880470..PON3........G..................AG
    rs9658135...PPARD.......A......................AG
    rs9658149...PPARD.......A......................AC
    rs10935780..RNF13.......C..CT
    rs9976946...RUNX1.......C..............CT
    rs17003493..SAMSN1......A......................AG
    rs35874481..SCARF1......A......................AG
    rs12144868..SCMH1.......C..............CT
    rs41276525..SCN5A.......A..............AG
    rs3917875...SELP........G..................CG
    rs1378220...SEMA6D......T......CT
    rs17284463..SEMA6D......G......AG
    rs17285093..SEMA6D......G......AG
    rs17356302..SEMA6D......G......AG
    rs17356420..SEMA6D......C......CT
    rs17356573..SEMA6D......A......AG
    rs17356726..SEMA6D......G......CG
    rs11664907..SERPINB12...G......................AG
    rs36049418..SLC12A3.....A..AG
    rs2328894...SLC17A4.....T..CT
    rs35888596..SLC22A1.....A......................AG
    rs724665....SLC25A40....A..AG
    rs28914833..SLC6A4......G..AG
    rs11568438..SLC7A7......A..............AG..AG
    rs11634219..SNORD115@...A..................AG
    rs17470471..SOX6........G..............GT
    rs1999661...SPATA31D1...T......................CT
    rs17648863..SPOPL.......C......CT
    rs929223....SPPL2C......A......................AG
    rs9860312...STAC........T..CT
    rs4361233...SUSD5.......G..AG
    rs17179194..SYNE2.......A......AG
    rs534564....TAOK3.......A......................AC
    rs2292969...TBCD........C..................CT
    rs526433....TECTA.......G..AG
    rs5029963...TNFAIP3.....G..................AG
    rs5745989...TNFRSF1B....A......AG
    rs45498900..TSC2........A......AC
    rs12884433..TSHR........T..CT
    rs12720355..TYK2........G......AG
    rs17863764..UGT1A8......G..............AG
    rs11574040..VDR.........G......................AG
    rs12355108..WDR11.......T..............CT
    rs17679361..WIPF2.......C..................CT
    rs35031397..WFS1........G......................CG
    rs34842534..XBP1........A..............AG......AG
    rs45471294..XDH.........T..............CT
    rs12798330..ZDHHC13.....G..................AG
    rs13271123..ZFPM2.......G......AG
    rs11011379..ZNF248......C..CT
  18. roxie60

    roxie60 Senior Member

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    Central Illinois, USA
    What were your PEX13 alleles? Was it GG?

  19. Valentijn

    Valentijn Activity Level: 3

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    Yup, nandixon had GG for that one.
  20. bel canto

    bel canto Senior Member

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    I don't understand how Ian's program works compared to what Prometheuse does in its "unique to you" report. The 4 alleles that I saw in Ian's program (based on my snps), I do not see in Prom. when I look all the way down to 5%.

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