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Rare allele data

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

  1. Valentijn

    Valentijn Activity Level: 3

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    At http://www.ianlogan.co.uk/23andme/23andMe_index2.htm someone has made a lovely program that goes through your results and shows the ones which have rare alleles (present in less than 1% of the population).

    While rarities are not necessarily indicative of a resulting dysfunction, they do present a nice place to start looking at things. Anyhow, maybe we can post our rare results here and compare to see if there's any trends?

    I've got 53 SNPs with rare alleles, two of which are homozygous. But one of those is apparently due to a mistake from 23andMe, so I'm really just homozygous for rs17526980 on the KIF13B gene. MA = Minor Alleles, and ones resulting in a missense or similar mutation are orange. My homozygous result is red. VAL = Valentijn's genotype.

    RSID.......GENE........MA..VAL
    rs12202093..??..........C..CT
    rs313273....??..........A..AG
    rs12845411..??..........T..CT
    rs11765511..??..........T..CT
    rs1364778...??..........A..AG
    rs2448326...??..........T..GT
    rs10036862..??..........A..AG
    rs1407268...??..........G..AG
    rs12154319..ABCB1.......A..AG
    rs56131651..ABCC2.......A..AG
    rs3730044...ACE.........A..AG
    rs7713754...AFF4........C..CT
    rs11239373..ANKRD30BP3..C..CT
    rs11246353..AP2A2.......A..AG
    rs41273157..ATP13A2.....T..CT
    rs11797182..BEX1........G..AG
    rs17394875..CACHD1......T..CT
    rs3848286...CES2........A..AG
    rs8176928...DNASE1......G..GG
    rs12534498..DTX2........A..AG
    rs2332284...PARP9.......C..CT
    rs5894......F2R.........G..GT
    rs9332688...F5..........A..AG
    rs428199....F9..........T..CT
    rs11239604..FAM21C......G..AG
    rs12194562..GRM1........C..CT
    rs62638620..GRM6........A..AG
    rs306781....GSN.........C..CT
    rs3218808...GTF2H4......T..CT
    rs3218816...GTF2H4......A..AG
    rs2857533...HOXD3.......T..GT
    rs1805128...KCNE1.......T..CT
    rs17526980..KIF13B......T..TT
    rs3212379...MC1R........T..CT
    rs1611772...MUC1........A..AG
    rs1799931...NAT2........A..AG
    rs4648039...NFKB1.......T..CT
    rs35722504..PARN........T..CT
    rs725522....PCSK1.......A..AG
    rs12195007..PHACTR1.....G..GT
    rs4135292...PPARG.......A..AG
    rs17219643..PTPRT.......T..CT
    rs36074402..RAB38.......A..AG
    rs10935780..RNF13.......C..CT
    rs36049418..SLC12A3.....A..AG
    rs2328894...SLC17A4.....T..CT
    rs724665....SLC25A40....A..AG
    rs28914833..SLC6A4......G..AG
    rs9860312...STAC........T..CT
    rs4361233...SUSD5.......G..AG
    rs526433....TECTA.......G..AG
    rs12884433..TSHR........T..CT
    rs11011379..ZNF248......C..CT
    merylg, nandixon and LaurieL like this.
  2. Sea

    Sea Senior Member

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    Interesting, I'll play. It might take me a while to figure out how to do it though. How did you find out about one being a mistake by 23andme Val?
  3. ukxmrv

    ukxmrv Senior Member

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    Thank you Valentijn!

    Thanks really interesting. I'm working through mine. So far only on Homo

    rs4844609 AT homo CR1 complement component (3b/4b) receptor 1 (Knops blood group) - missense T2060S ('le') AT' MAF = 0.00731 Possibly 5% in Europe and Asia and absent from Africa. The change T<>S is uncommon and the homozygous form could be significant.
  4. Valentijn

    Valentijn Activity Level: 3

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    Looks like that one is extremely rare (you're AA?). http://hmg.oxfordjournals.org/content/21/10/2377.full has a lot of discussion about it, and http://www.ncbi.nlm.nih.gov/gene/1378 has some background info on the gene (though that doesn't mean that this SNP will necessarily affect the gene is those ways). Sounds like it can be involved in a lot of immune and autoimmune issues.
    ukxmrv likes this.
  5. merylg

    merylg Senior Member

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    This is interesting Valentijn. I can't figure out how to use ian's program yet, so I thought I'd look at my results for the one's you have found. I have a few similar.
    I have:
    For rs17526980..KIF13B.. T...CT (Are you saying that is an error by 23andMe and my result should be homozygous TT ???)

    Here's some info on KIF13B
    http://www.phosphosite.org/proteinAction.do?id=16093&showAllSites=true
    Valentijn likes this.
  6. Valentijn

    Valentijn Activity Level: 3

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    Searching for it brought up other peoples' (who chose to share them) results from the rare allele site, with a comment that it's a mistake from 23andMe.
  7. Valentijn

    Valentijn Activity Level: 3

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    It's a different one that gives a wrong reading (rs8176928...DNASE1). But definitely interesting that you're heterozygous on the KIF13B, since even that is pretty uncommon. Not a lot is known about the gene, but it sounds like it's involved in the framework/support structure inside cells, and possibly transporting specific types of proteins. It's too technical for me to understand yet, though :p
    merylg likes this.
  8. Valentijn

    Valentijn Activity Level: 3

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    Updated rare allele table, based on the couple results people have posted here:
    RSID.......GENE........MA.VAL.UKX.MER
    rs12202093..??..........C..CT
    rs313273....??..........A..AG
    rs12845411..??..........T..CT
    rs11765511..??..........T..CT
    rs1364778...??..........A..AG
    rs2448326...??..........T..GT
    rs10036862..??..........A..AG
    rs1407268...??..........G..AG
    rs12154319..ABCB1.......A..AG
    rs56131651..ABCC2.......A..AG
    rs3730044...ACE.........A..AG
    rs7713754...AFF4........C..CT
    rs11239373..ANKRD30BP3..C..CT
    rs11246353..AP2A2.......A..AG
    rs41273157..ATP13A2.....T..CT
    rs11797182..BEX1........G..AG
    rs17394875..CACHD1......T..CT
    rs3848286...CES2........A..AG
    rs4844609...CR1.........A..TT..AA
    rs8176928...DNASE1......G..GG
    rs12534498..DTX2........A..AG
    rs2332284...PARP9.......C..CT
    rs5894......F2R.........G..GT
    rs9332688...F5..........A..AG
    rs428199....F9..........T..CT
    rs11239604..FAM21C......G..AG
    rs12194562..GRM1........C..CT
    rs62638620..GRM6........A..AG
    rs306781....GSN.........C..CT
    rs3218808...GTF2H4......T..CT
    rs3218816...GTF2H4......A..AG
    rs2857533...HOXD3.......T..GT
    rs1805128...KCNE1.......T..CT
    rs17526980..KIF13B......T..TT......CT
    rs3212379...MC1R........T..CT
    rs1611772...MUC1........A..AG
    rs1799931...NAT2........A..AG
    rs4648039...NFKB1.......T..CT
    rs35722504..PARN........T..CT
    rs725522....PCSK1.......A..AG
    rs12195007..PHACTR1.....G..GT
    rs4135292...PPARG.......A..AG
    rs17219643..PTPRT.......T..CT
    rs36074402..RAB38.......A..AG
    rs10935780..RNF13.......C..CT
    rs36049418..SLC12A3.....A..AG
    rs2328894...SLC17A4.....T..CT
    rs724665....SLC25A40....A..AG
    rs28914833..SLC6A4......G..AG
    rs9860312...STAC........T..CT
    rs4361233...SUSD5.......G..AG
    rs526433....TECTA.......G..AG
    rs12884433..TSHR........T..CT
    rs11011379..ZNF248......C..CT
  9. bel canto

    bel canto Senior Member

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    Is there a way to use Ian's program on a mac?
  10. Valentijn

    Valentijn Activity Level: 3

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    The program is on his website. So you cut and past the 23andMe data into that, then hit four buttons in the right order, then you get the results.
  11. Valentijn

    Valentijn Activity Level: 3

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    How to get your rare allele data:

    PART I: Download your 23andMe results to your computer
    1) Go to https://www.23andme.com/you/download/ and enter your email address and 23andMe password
    2) Enter your password again, and your "Secret answer"
    3) Select your profile
    4) Select All DNA
    5) Click "download data"
    6) Wait 10-20 seconds, then select "open with" windows explorer
    7) Wait a while during the download. Then the folder with "genome_Your_Name_Full_2013_etc" should open itself up.

    PART II: Putting the file somewhere that you can find it again
    1) Right click on the file, and select "copy"
    2) Go to your desktop (or wherever you want to put it) and right click then select "paste"

    (Now you can open this file if you want to search for specific genes. Just be sure not to save it any time you close it. It can take a minute or two to open, because it's a huge file.)

    PART III: Getting a list of your rare alleles
    1) Go to http://www.ianlogan.co.uk/23andme/minor_allele_data.htm
    2) Select "Chrs 1-3" from the drop down menu
    3) Click the top "read" button, then click "analyse" (if something goes wrong here, select "-" from the drop down menu, hit the top "clear" button, and go back to step 2). You should have "Summary of data" blah blah blah in the top window.
    4) Open your 23andMe file - this takes a couple minutes.
    5) Click to the left of your first rsid (rs4477212), so your cursor is located there.
    6) Hold down the shift key until told to let go of it
    7) Hold down the vertical scroll bar and scroll down until you find where chromosome 3 ends and 4 begins (NOT clicking anywhere in the document in the process). You'll probably need to "page up" or "page down" a bit (PgUp/PgDn on some keyboards) once the scroll bar isn't precise enough.
    8)Click on the right side of the final chromosome 3 row while still holding down the shift key. This should select the entirety of chromosome 1-3.
    9) Let go of the shift key
    10) Right click on the highlighted text and select "copy"
    11) Go back to the minor allele data page and right click in the bottom (bigger) box and select "paste". Then wait 5-10 seconds for it copy into the box.
    12) Hit the bottom "read" button, then "match data". Then you should get a list of your rare alleles in that bottom box.

    Part IV: Making a list of your rare alleles
    1) Open a new text, word, or excel document
    2) Select your results by dragging over them with your mouse cursor
    3) Right-click the highlighted text
    4) Go to the document you just opened, right click on the empty page area, and select "paste"

    Part V: Rinse and Repeat
    1) Hit the "clear" buttons on the top and bottom windows on the rare allele data page.
    2) Select the next chromosome, and repeat from Part III step 2 through Part IV.

    Or send me a private message and I can give you my email address and you can send me your file and I can run it through and get the results to send back to you :p
    ukxmrv and merylg like this.
  12. Sea

    Sea Senior Member

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    I managed to get mine, though I haven't really looked through them yet or done any comparisons to the others here

    rs17349278 at Chr1:4836929 gave 'GT' The minor allele is 'T' with a MAF = 0.00457
    rs34248917 at Chr1:5951013 gave 'CT' The minor allele is 'T' with a MAF = 0.00457
    rs1053360 at Chr1:25628088 gave 'AG' The minor allele is 'A' with a MAF = 0.00000
    rs12144868 at Chr1:41539745 gave 'CT' The minor allele is 'C' with a MAF = 0.00000
    rs17410855 at Chr1:46086766 gave 'CT' The minor allele is 'T' with a MAF = 0.00228
    rs28414989 at Chr1:47399879 gave 'CC' The minor allele is 'C' with a MAF = 0.00999
    rs1109918 at Chr1:67862482 gave 'AG' The minor allele is 'G' with a MAF = 0.00822.
    rs12751479 at Chr1:98056007 gave 'GT' The minor allele is 'T' with a MAF = 0.00228
    rs2231855 at Chr1:157095853 gave 'AG' The minor allele is 'G' with a MAF = 0.00776.
    rs28369860 at Chr1:171165803 gave 'DI' The minor allele is 'D' with a MAF = 0.00950
    rs28384848 at Chr1:171224812 gave 'CT' The minor allele is 'C' with a MAF = 0.00502

    rs45471294 at Chr2:31600017 gave 'CT' The minor allele is 'T' with a MAF = 0.00914.
    rs34409923 at Chr2:97368670 gave 'AG' The minor allele is 'A' with a MAF = 0.00548
    rs17632157 at Chr2:105551399 gave 'CT' The minor allele is 'T' with a MAF = 0.00914
    rs17863764 at Chr2:234529415 gave 'AG' The minor allele is 'G' with a MAF = 0.00365

    rs13071214 at Chr3:1036715 gave 'CT' The minor allele is 'C' with a MAF = 0.00731
    rs17786289 at Chr3:1771198 gave 'AG' The minor allele is 'A' with a MAF = 0.00914
    rs17193729 at Chr3:1789200 gave 'AG' The minor allele is 'G' with a MAF = 0.00959
    rs1497 at Chr3:3191813 gave 'GT' The minor allele is 'G' with a MAF = 0.00914
    rs41276525 at Chr3:38655290 gave 'AG' The minor allele is 'A' with a MAF = 0.00000

    rs4968 at Chr4:2931190 gave 'CT' The minor allele is 'T' with a MAF = 0.00319
    rs17322140 at Chr4:139993175 gave 'AG' The minor allele is 'A' with a MAF = 0.00500

    rs10036862 at Chr5:124665264 gave 'AG' The minor allele is 'A' with a MAF = 0.00914

    rs12189802 at Chr6:27714048 gave 'CT' The minor allele is 'T' with a MAF = 0.00000
    rs11967812 at Chr6:29835632 gave 'CT' The minor allele is 'C' with a MAF = 0.00999
    rs1407268 at Chr6:153064110 gave 'AG' The minor allele is 'G' with a MAF = 0.00914

    rs8177173 at Chr7:142561922 gave 'AG' The minor allele is 'A' with a MAF = 0.00457

    rs35909721 at Chr8:2324045 gave 'AG' The minor allele is 'A' with a MAF = 0.00776
    rs8178216 at Chr8:48719844 gave 'AG' The minor allele is 'A' with a MAF = 0.00045.

    rs34552278 at Chr9:33447553 gave 'AG' The minor allele is 'A' with a MAF = 0.00548.
    rs1699499 at Chr9:98008381 gave 'CT' The minor allele is 'C' with a MAF = 0.00959
    rs306781 at Chr9:124042944 gave 'CT' The minor allele is 'C' with a MAF = 0.00959
    rs11549260 at Chr9:130928633 gave 'CT' The minor allele is 'T' with a MAF = 0.00594

    rs8177788 at Chr10:5994841 gave 'CT' The minor allele is 'T' with a MAF = 0.00639.
    rs17556220 at Chr10:70716061 gave 'CT' The minor allele is 'T' with a MAF = 0.00685
    rs17173698 at Chr10:89468953 gave 'AG' The minor allele is 'A' with a MAF = 0.00685
    rs17449755 at Chr10:94669531 gave 'GT' The minor allele is 'T' with a MAF = 0.00274
    rs12355108 at Chr10:122633421 gave 'CT' The minor allele is 'T' with a MAF = 0.00776
    rs11199654 at Chr10:122684069 gave 'AG' The minor allele is 'A' with a MAF = 0.00776

    rs17470471 at Chr11:16442456 gave 'GT' The minor allele is 'G' with a MAF = 0.00822

    rs1799954 at Chr13:32914592 gave 'CT' The minor allele is 'T' with a MAF = 0.00137
    rs2303965 at Chr13:109704760 gave 'CT' The minor allele is 'T' with a MAF = 0.00868.

    rs11568438 at Chr14:23282336 gave 'AG' The minor allele is 'A' with a MAF = 0.00776.

    rs8176928 at Chr16:3706185 gave 'GG' The minor allele is 'G' with a MAF = 0.00457

    rs11879596 at Chr19:11537377 gave 'AG' The minor allele is 'A' with a MAF = 0.00594
    rs11673485 at Chr19:39727668 gave 'GT' The minor allele is 'T' with a MAF = 0.00639

    rs17208220 at Chr21:15855286 gave 'CT' The minor allele is 'T' with a MAF = 0.00777
    rs9976946 at Chr21:36208062 gave 'CT' The minor allele is 'C' with a MAF = 0.00639

    rs34842534 at Chr22:29191898 gave 'AG' The minor allele is 'A' with a MAF = 0.00090

    rs1801316 at ChrX:119005968 gave 'CG' The minor allele is 'C' with a MAF = 0.00120
    rs2301187 at ChrX:152340657 gave 'GT' The minor allele is 'G' with a MAF = 0.00000
    rs6627746 at ChrX:152437627 gave 'CT' The minor allele is 'T' with a MAF = 0.00000

    How do I tidy it up and make it look neat like yours Val, without lots of typing?
    Valentijn likes this.
  13. nandixon

    nandixon Senior Member

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    Here are my results. Only one homozygous finding, for rs1177230 (GG) on the PEX13 gene.

    Chromosomes 1-3
    rs12751479 (Gene = DPYD) GT (Minor allele = T, MAF = 0.00228)
    rs12094954 (Intergenic) CT (T, 0.00548)
    rs3917875 (SELP) CG (G, 0.00182)
    rs689469 (PTGS2) CT (T, 0.00914)
    rs4648298 (PTGS2) CT (C, 0.00914)
    rs1177230 (PEX13) GG (G, 0.00731) ***
    rs34409923 (FER1L5) AG (A, 0.00548)
    rs13096071 (Intergenic) CT (C, 0.00776)

    Chromosomes 4-7
    rs17473279 (Intergenic) AG (G, 0.00822)
    rs3213102 (IL12B) CT (T, 0.00731)
    rs56106312 (GCNT2) AG (A, 0.00457)
    rs5029963 (TNFAIP3) AG (G, 0.00319)
    rs12527982 (LOC100505519) CT (T, 0.00182)
    rs17880470 (PON3) AG (G, 0.00228)
    rs4732359 (LOC100132310) AG (A, 0.00137)
    rs55960271 (CLCN1) CT (T, 0.00000)

    Chromosomes 8-12
    rs60156239 (NEFL) AG (A, 0.00319)
    rs11781640 (KIFC2, FOXH1) CT (T, 0.00137)
    rs1699499 (FANCC) CT (C, 0.00959)
    rs12357104 (RET) CT (T, 0.00639)
    rs9658682 (FAS) AG (G, 0.00685)
    rs11572144 (CYP2C8) AG (A, 0.00365)
    rs12798330 (ZDHHC13) AG (G, 0.00822)
    rs17581686 (Intergenic) CT (T, 0.00319)
    rs11227700 (KDM2A) AG (A, 0.00457)
    rs11601245 (CORO1B) CT (T, 0.00365)
    rs11169088 (FAM186B) AG (A, 0.00319)
    rs58843120 (ABCB9) GT (T, 0.00319)

    Chromosomes 13-22
    rs2812230 (Intergenic) CT (C, 0.00639)
    rs11568438 (SLC7A7) AG (A, 0.00776)
    rs17322331 (Intergenic) CT (T, 0.00959)
    rs2738415 (ESR2) CT (T, 0.00822)
    rs11623598 (GPHN) CT (T, 0.00959)
    rs11634219 (SNRPN, SNORD115@) AG (A, 0.00639)
    rs8042511 (Intergenic) AC (C, 0.00868)
    rs220378 (Intergenic) AC (C, 0.00914)
    rs4986970 (LCAT) AT (T, 0.00914)
    rs17678817 (MSL1) CT (T, 0.00776)
    rs17679086 (CASC3) AG (G, 0.00776)
    rs17679361 (WIPF2) CT (C, 0.00776)
    rs4135012 (CDC6) AG (A, 0.00776)
    rs11568605 (ABCC3) CT (T, 0.00457)
    rs4988346 (BRIP1) CT (T, 0.00500)
    rs2292969 (TBCD) CT (C, 0.00457)
    rs7247965 (Intergenic) AC (A, 0.00594)
    Valentijn likes this.
  14. Valentijn

    Valentijn Activity Level: 3

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    Sea : I've added you to the table :D It looks like we have three heterozygous SNPs in common - two SNPs on non-gene locations ("??"), and one on GSN.

    RSID.......GENE........MA.VAL.UKX.MER.SEA
    rs10036862..??..........A..AG..........AG
    rs11199654..??..........A..............AG
    rs11673485..??..........T..............GT
    rs11765511..??..........T..CT
    rs11967812..??..........C..............CT
    rs12189802..??..........T..............CT
    rs12202093..??..........C..CT
    rs12845411..??..........T..CT
    rs13071214..??..........C..............CT
    rs1364778...??..........A..AG
    rs1407268...??..........G..AG..........AG
    rs17193729..??..........G..............AG
    rs17208220..??..........T..............CT
    rs17632157..??..........T..............CT
    rs17786289..??..........A..............AG
    rs2301187...??..........G..............GT
    rs2303965...??..........T..............CT
    rs2448326...??..........T..GT
    rs313273....??..........A..AG
    rs35909721..??..........A..............AG
    rs6627746...??..........T..............CT
    rs12154319..ABCB1.......A..AG
    rs56131651..ABCC2.......A..AG
    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
    rs41273157..ATP13A2.....T..CT
    rs11797182..BEX1........G..AG
    rs1799954...BRCA2.......T..............CT
    rs17394875..CACHD1......T..CT
    rs17410855..CCD17.......T..............CT
    rs11879596..CCDC151.....A..............AG
    rs3848286...CES2........A..AG
    rs11549260..CIZ1........T..............CT
    rs4844609...CR1.........A......AA
    rs1497......CRBN........G..............GT
    rs28414989..CYP4A11.....C..............CC
    rs17556220..DDX21.......T..............CT
    rs8176928...DNASE1......G
    rs12751479..DPYD........T..............GT
    rs12534498..DTX2........A..AG
    rs2332284...PARP9.......C..CT
    rs17322140..ELF2........A..............AG
    rs8177173...EPHB6.......A..............AG
    rs2231855...ETV3........G..............AG
    rs17449755..EXOC6.......T..............GT
    rs5894......F2R.........G..GT
    rs9332688...F5..........A..AG
    rs428199....F9..........T..CT
    rs11239604..FAM21C......G..AG
    rs1699499...FANCC.......C..............CT
    rs34409923..FER1L5......A..............AG
    rs28384848..FMO1........C..............CT
    rs28369860..FMO2........D..............DI
    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
    rs1109918...IL12RB2.....G..............AG
    rs8177788...IL15RA......T..............CT
    rs1805128...KCNE1.......T..CT
    rs17526980..KIF13B......T..TT......CT
    rs3212379...MC1R........T..CT
    rs1611772...MUC1........A..AG
    rs1799931...NAT2........A..AG
    rs1801316...NDUFA1......C..............CG
    rs4648039...NFKB1.......T..CT
    rs34248917..NPHP4.......T..............CT
    rs17173698..PAPSS2......A..............AG
    rs35722504..PARN........T..CT
    rs725522....PCSK1.......A..AG
    rs12195007..PHACTR1.....G..GT
    rs4135292...PPARG.......A..AG
    rs8178216...PRKDC.......A..............AG
    rs17219643..PTPRT.......T..CT
    rs36074402..RAB38.......A..AG
    rs1053360...RHD.........A..............AG
    rs10935780..RNF13.......C..CT
    rs9976946...RUNX1.......C..............CT
    rs12144868..SCMH1.......C..............CT
    rs41276525..SCN5A.......A..............AG
    rs36049418..SLC12A3.....A..AG
    rs2328894...SLC17A4.....T..CT
    rs724665....SLC25A40....A..AG
    rs28914833..SLC6A4......G..AG
    rs11568438..SLC7A7......A..............AG
    rs17470471..SOX6........G..............GT
    rs9860312...STAC........T..CT
    rs4361233...SUSD5.......G..AG
    rs526433....TECTA.......G..AG
    rs12884433..TSHR........T..CT
    rs17863764..UGT1A8......G..............AG
    rs12355108..WDR11.......T..............CT
    rs34842534..XBP1........A..............AG
    rs45471294..XDH.........T..............CT
    rs11011379..ZNF248......C..CT
    Sea likes this.
  15. Valentijn

    Valentijn Activity Level: 3

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    Amersfoort, Netherlands
    nandixon,You have four of the same rare alleles as Sea, located on DPYD, FANCC, FER1L5, and SLC7A7.

    SNPs variations shared by at least two people are now highlighted in red.

    RSID.......GENE........MA.VAL.UKX.MER.SEA.NAN
    rs10036862..??..........A..AG..........AG
    rs11199654..??..........A..............AG
    rs11673485..??..........T..............GT
    rs11765511..??..........T..CT
    rs11967812..??..........C..............CT
    rs12094954..??..........T.................CT
    rs12189802..??..........T..............CT
    rs12202093..??..........C..CT
    rs12845411..??..........T..CT
    rs13071214..??..........C..............CT
    rs13096071..??..........C.................CT
    rs1364778...??..........A..AG
    rs1407268...??..........G..AG..........AG
    rs17193729..??..........G..............AG
    rs17208220..??..........T..............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
    rs2812230...??..........C.................CT
    rs313273....??..........A..AG
    rs35909721..??..........A..............AG
    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
    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
    rs41273157..ATP13A2.....T..CT
    rs11797182..BEX1........G..AG
    rs1799954...BRCA2.......T..............CT
    rs4988346...BRIP1.......T.................CT
    rs17394875..CACHD1......T..CT
    rs17679086..CASC3.......G.................AG
    rs17410855..CCD17.......T..............CT
    rs11879596..CCDC151.....A..............AG
    rs4135012...CDC6........A.................AG
    rs3848286...CES2........A..AG
    rs11549260..CIZ1........T..............CT
    rs55960271..CLCN1.......T.................CT
    rs11601245..CORO1B......T.................CT
    rs4844609...CR1.........A......AA
    rs1497......CRBN........G..............GT
    rs11572144..CYP2C8......A.................AG
    rs28414989..CYP4A11.....C..............CC
    rs17556220..DDX21.......T..............CT
    rs8176928...DNASE1......G
    rs12751479..DPYD........T..............GT.GT
    rs12534498..DTX2........A..AG
    rs2332284...PARP9.......C..CT
    rs17322140..ELF2........A..............AG
    rs8177173...EPHB6.......A..............AG
    rs2738415...ESR2........T.................CT
    rs2231855...ETV3........G..............AG
    rs17449755..EXOC6.......T..............GT
    rs5894......F2R.........G..GT
    rs9332688...F5..........A..AG
    rs428199....F9..........T..CT
    rs11169088..FAM186B.....A.................AG
    rs11239604..FAM21C......G..AG
    rs1699499...FANCC.......C..............CT.CT
    rs9658682...FAS.........G.................AG
    rs34409923..FER1L5......A..............AG.AG
    rs28384848..FMO1........C..............CT
    rs28369860..FMO2........D..............DI
    rs56106312..GCNT2.......A.................AG
    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
    rs4986970...LCAT........T.................AT
    rs4732359...LOC100132310A.................AG
    rs12527982..LOC100505519T.................CT
    rs3212379...MC1R........T..CT
    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
    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
    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
    rs9860312...STAC........T..CT
    rs4361233...SUSD5.......G..AG
    rs2292969...TBCD........C.................CT
    rs526433....TECTA.......G..AG
    rs5029963...TNFAIP3.....G.................AG
    rs12884433..TSHR........T..CT
    rs17863764..UGT1A8......G..............AG
    rs12355108..WDR11.......T..............CT
    rs17679361..WIPF2.......C.................CT
    rs34842534..XBP1........A..............AG
    rs45471294..XDH.........T..............CT
    rs12798330..ZDHHC13.....G.................AG
    rs11011379..ZNF248......C..CT
    Sea and nandixon like this.
  16. Valentijn

    Valentijn Activity Level: 3

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    Amersfoort, Netherlands
    I've calculated the odds of us having these shared alleles ... and some of them are astronomically small. If I messed up on the math (Graham ?) or can improve it please let me know. :D

    rs10036862 (??)
    1.0% prevelance of the minor allele. 1 in 100 people have it. The probability that two random people meeting have that same allele is 1 in 10,000.

    rs1407268 (??)
    1.0% prevelance of the minor allele. 1 in 100 people have it. The probability that two random people meeting have that same allele is 1 in 10,000.

    rs12751479 (DPYD)
    0.1% prevalence of the minor allele. 1 in 1,000 people have it. The probability that two random people meeting have that same allele is 1 in 1,000,000.

    rs1699499 (FANCC)
    1.0% prevelance of the minor allele. 1 in 100 people have it. The probability that two random people meeting have that same allele is 1 in 10,000.

    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 15,625.

    rs306781 (GSN)
    1.0% prevelance of the minor allele. 1 in 100 people have it. The probability that two random people meeting have that same allele is 1 in 10,000.

    rs17526980 (KIF13B)
    0.7% prevalence of the minor allele. 1 in 143 people have it. Calulated 0.005% prevalance of two minor alleles in one person. Calculated that 1 in 20,408 people have it. The probabability that one random person has two minor alleles and that the first random person they meet has one minor allele is 1 in 2,915,451.

    rs11568438 (SLC7A7)
    0.7% prevalence of the minor allele. 1 in 143 people have it. The probability that two random people meeting have that same allele is 1 in 20,408.

    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 we would both have that minor allele and the GSN minor allele is 1 in 100,000,000.

    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 they would both have these 4 minor alleles is 1 in 3,188,000,000,000,000,000.

    The probability of two random people sharing some of these alleles borders on the impossible. Thus it would seem that shared characteristics (having ME/CFS) are very likely related to having at least some of these shared alleles.
    Sea likes this.
  17. Sea

    Sea Senior Member

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    NSW Australia
    Wow, they are some remarkable figures.
  18. ukxmrv

    ukxmrv Senior Member

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    London
    Hi Val,

    Thanks for all the number crunching. Much appreciated!

    I'm still going on mine but these are the extra ones so far. There is one mistake I can see already (the column marked ???) and I'll rerun that one and correct. More to come as well

    UKXMRV

    rs5745989 AG A
    rs4949212 GT G
    rs11577810 CT T
    rs17570718 AC C
    rs12117552 AG A
    rs10495765 AG G
    rs17648863 CT ???
    rs13006003 AG A
    rs6054 CT T
    rs17613128 GT T
    rs2243072 CT T
    rs28043 AG G
    rs4151681 AG A
    rs11751917 AG A
    rs17793768 CT T
    rs2513812 GT G
    rs13271123 AG G
    rs17273542 AG A
    rs273466 AG A
    rs273469 CT C
    rs12554509 CT T
    rs11239373 CT C
    rs11239604 AG G
    rs35678986 GT G
    rs3212861 AG A
    Valentijn likes this.
  19. ukxmrv

    ukxmrv Senior Member

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    London
    What is the normal function of the FAM134B gene?

    The FAM134B gene provides instructions for making a protein important for the survival of sensory and autonomic nerve cells (neurons). Sensory neurons transmit pain, touch, and temperature sensations. Autonomic neurons help control involuntary functions of the body such as heart rate and blood pressure. Within neurons, the FAM134B protein is found in a structure called the Golgi apparatus, which is important for distribution of proteins to the cell. However, the function of the FAM134B protein is unknown. Studies have shown that neurons in which the FAM134B protein is absent die by a process of self-destruction called apoptosis.

    How are changes in the FAM134B gene related to health conditions?

    hereditary sensory and autonomic neuropathy type II - caused by mutations in the FAM134B gene
    Mutations in the FAM134B gene are responsible for one type of hereditary sensory and autonomic neuropathy type II (HSAN2) called HSAN2B. People with HSAN2B lose the ability to feel pain or sense hot and cold. The FAM134B gene mutations may lead to an abnormally short and nonfunctional protein. The lack of FAM134B protein causes neurons to undergo apoptosis, which reduces the overall number of sensory and autonomic neurons. The loss of neurons results in the signs and symptoms of HSAN2B.
    Journeyman and Valentijn like this.
  20. Valentijn

    Valentijn Activity Level: 3

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    So far you just have rs11239604 (FAM21C) in common with another patient - me! :D

    I've got results arranged in alphabetical order by gene, so it might be a little easier to see dysfunctions in the same processes, even if the relevant SNPs are on different genes. But maybe we can go through the bunch of them at some point and make a list of keywords for each, like "actin" or "serotonin", etc, to see if there's shared vulnerabilities that are less obvious.
    Sea and ukxmrv like this.

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