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First Direct Evidence of Neuroinflammation - 'Encephalitis' - in ME/CFS
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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

    Messages:
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    Amersfoort, Netherlands
    Updated to include the results from kday . Results shared by more than one forum member are shown with a bold, underlined, and red rsID. Missense and other mutations are shown with a bold, underlined, and orange MA (minor allele). Homozygous rare results are shown as bold, underlined, and red alleles for that user.

    Kday has one shared result with another forum member (me :D) at rs5894 on the F2R gene. The "i" numbers have been converted to rsIDs. i4000440 = rs138058578, i5008776 = rs76157638 (http://omim.org/entry/601691#0001) and i5008213 = rs17473.


    RSID.......GENE........MA.VAL.UKX.MER.SEA.NAN.GyD.KDA
    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
    rs11799701..??..........G..........................AG
    rs11967812..??..........C..............CT
    rs12094954..??..........T..................CT
    rs12189802..??..........T..............CT
    rs12202093..??..........C..CT
    rs12554509..??..........T......CT
    rs12845411..??..........T..CT
    rs13006003..??..........A......AG
    rs13064618..??..........T..........................CT
    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
    rs17823699..??..........C..........................CT
    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
    rs76157638..ABCA4.......G..........................CG
    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
    rs1799952...BRCA2.......A..........................AG
    rs1799954...BRCA2.......T..............CT
    rs4988346...BRIP1.......T..................CT
    rs2234548...BRWD1.......C..........................CT
    rs11216131..BUD13.......A..........................AC
    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
    rs13264103..CHCHD7......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
    rs943639....EPS8L3......G..........................AG
    rs2738415...ESR2........T..................CT
    rs2231855...ETV3........G..............AG
    rs17449755..EXOC6.......T..............GT
    rs5894......F2R.........G..GT .....................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
    rs9282671...FAM82A1.....T..........................AT
    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
    rs4924733...FRMD5.......T..........................CT
    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
    rs11563711..GRM8........A..........................AG
    rs306781....GSN.........C..CT..........CT
    rs8191451...GSTP1.......A..........................AG
    rs3218808...GTF2H4......T..CT
    rs3218816...GTF2H4......A..AG
    rs138058578.HEXA........A..........................AG
    rs2857533...HOXD3.......T..GT
    rs3783538...IL1A........G..........................AG
    rs3213102...IL12B.......T..................CT
    rs1109918...IL12RB2.....G..............AG
    rs8177788...IL15RA......T..............CT
    rs11574627..IL2RG.......T......................CT
    rs13167382..ITK.........A......................AG
    rs13187882..ITK.........G......................AG
    rs8192839...JHDM1D......T..........................CT
    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
    rs17217321..LOC100128164T..........................CT
    rs4732359...LOC100132310A..................AG
    rs12527982..LOC100505519T..................CT
    rs34950679..LOC100996307C..........................CG
    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
    rs11868845..NLRP1.......C..........................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
    rs17473.....SERPINA3....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
    rs16893137..TAPT1.......C..........................CT
    rs2292969...TBCD........C..................CT
    rs3735354...TBXAS1......A..........................AG
    rs526433....TECTA.......G..AG
    rs3093647...TMEM50A.....T..........................CT
    rs5029963...TNFAIP3.....G..................AG
    rs5745989...TNFRSF1B....A......AG
    rs11573970..TNFRSF14....G..........................GG
    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
    ukxmrv likes this.
  2. Valentijn

    Valentijn Activity Level: 3

    Messages:
    6,034
    Likes:
    8,385
    Amersfoort, Netherlands
    Updated to add allyb's results. Rare SNPs shared by multiple forum members are shown by RS numbers (RSID) in red, with italics for the one with more than two members having it. Missense and similar mutations are shown in orange minor alleles (MA), and homozygous genotypes are shown in red for the users which have them.


    RSID.......GENE........MA.VAL.UKX.MER.SEA.NAN.GyD.KDA.ALY
    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
    rs11799701..??..........G..........................AG
    rs11967812..??..........C..............CT
    rs12094954..??..........T..................CT
    rs12189802..??..........T..............CT
    rs12202093..??..........C..CT
    rs12554509..??..........T......CT......................CT
    rs12845411..??..........T..CT
    rs13006003..??..........A......AG
    rs13064618..??..........T..........................CT
    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
    rs17823699..??..........C..........................CT
    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
    rs76157638..ABCA4.......G..........................CG
    rs12154319..ABCB1.......A..AG
    rs11772720..ABCB5.......C......................CT......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..........................CT
    rs34203073..AGGF1.......A......................AG
    rs34938955..AHR.........T......................CT
    rs17349278..AJAP1.......T..............GT
    rs41286234..ALDH8A1.....C..............................CG
    rs11571365..ALOX12......T......................CT
    rs11239373..ANKRD30BP3..C..CT
    rs11246353..AP2A2.......A..AG
    rs28931578..APOE........A..............................AG
    rs34552278..AQP3........A..............AG
    rs17318151..ARID1B......G..............................AG
    rs2306852...ASUN........G..............................AG
    rs11697265..ATP5E.......C......CT
    rs2231943...ATP5SL......T......................CT
    rs41273157..ATP13A2.....T..CT
    rs3738888...BARD1.......A..............................AG
    rs11797182..BEX1........G..AG..........................AG
    rs11090143..BIK.........T......CT
    rs1799952...BRCA2.......A..........................AG
    rs1799954...BRCA2.......T..............CT
    rs4988346...BRIP1.......T..................CT..........CT
    rs2234548...BRWD1.......C..........................CT
    rs11216131..BUD13.......A..........................AC
    rs11055389..C12orf36....A......AG......................AG
    rs59286323..CACNA1H.....T......CT
    rs17394875..CACHD1......T..CT
    rs17679086..CASC3.......G..................AG
    rs17410855..CCD17.......T..............CT
    rs13385919..CCDC142.....T..............................CT
    rs11879596..CCDC151.....A..............AG
    rs3212861...CCND1.......A......AG
    rs12971873..CD37........A..............................AC
    rs13207595..CD109.......G..............................AG
    rs4135012...CDC6........A..................AG
    rs2582563...CEP170B.....T......................CT
    rs3848286...CES2........A..AG
    rs13264103..CHCHD7......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
    rs17736439..EIF4EBP1....G..............................AG
    rs17322140..ELF2........A..............AG
    rs17630626..EMX2OS......T..............................GT
    rs8177173...EPHB6.......A..............AG......AG
    rs943639....EPS8L3......G..........................AG
    rs2738415...ESR2........T..................CT
    rs2231855...ETV3........G..............AG
    rs17449755..EXOC6.......T..............GT
    rs5894......F2R.........G..GT .....................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
    rs9282671...FAM82A1.....T..........................AT
    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
    rs4924733...FRMD5.......T..........................CT
    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
    rs11563711..GRM8........A..........................AG
    rs306781....GSN.........C..CT..........CT
    rs8191451...GSTP1.......A..........................AG
    rs3218808...GTF2H4......T..CT
    rs3218816...GTF2H4......A..AG
    rs61749670..GUCY2D......D..............................DI
    rs35939489..HBB.........G..............................GT
    rs138058578.HEXA........A..........................AG
    rs2857533...HOXD3.......T..GT
    rs1990554...ICA1........A..............................AC
    rs3783538...IL1A........G..........................AG
    rs3213102...IL12B.......T..................CT..........CT
    rs1109918...IL12RB2.....G..............AG
    rs8177788...IL15RA......T..............CT
    rs11574627..IL2RG.......T......................CT
    rs13167382..ITK.........A......................AG
    rs13187882..ITK.........G......................AG
    rs8192839...JHDM1D......T..........................CT
    rs1805128...KCNE1.......T..CT
    rs11227700..KDM2A.......A..................AG
    rs565156....KIAA1107....C..............................AC
    rs17526980..KIF13B......T..TT......CT
    rs11781640..KIFC2.FOXH1.T..................CT..CT
    rs2227122...KL..........T..............................GT
    rs11577810..KPNA6.......T......CT
    rs35678986..KRTAP5-4....G......GT
    rs4986970...LCAT........T..................AT
    rs11936089..LCORL.......T..............................CT
    rs61737308..LINGO1......T......CT
    rs735262....LINK00032...T......................CT
    rs12117552..LMNA........A......AG
    rs58992194..LMNB2.......T..............................CT
    rs17217321..LOC100128164T..........................CT
    rs4732359...LOC100132310A..................AG
    rs12527982..LOC100505519T..................CT
    rs34950679..LOC100996307C..........................CG
    rs10972206..LOC101929739G..............................AG
    rs11239373..LOC338579...C......CT
    rs4949212...LOC441880...G......GT
    rs11564181..LRRK2.......A......................AT
    rs3025980...M1AP........T..............................CT
    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
    rs17393302..MFSD8.......T..............................CT
    rs28937908..MLCYD.......C......CT
    rs1056784...MMP19.......A......AG
    rs17273542..MPDZ........A......AG
    rs63750757..MSH2........A......................AG
    rs17678817..MSL1........T..................CT
    rs1611772...MUC1........A..AG
    rs12149514..MVP.........G..............................AG
    rs659497....NAGLU.......T..............................CT
    rs1799931...NAT2........A..AG
    rs12817914..NAV3........T......................CT
    rs11755226..NCR3........G..............................GT
    rs1801316...NDUFA1......C..............CG
    rs60156239..NEFL........A..................AG
    rs4648039...NFKB1.......T..CT
    rs11191279..NFKB2.......T......................CT......CT
    rs28909970..NGB.........T..............................GT
    rs11868845..NLRP1.......C..........................CT
    rs3730014...NOS2........A..............................AG
    rs34248917..NPHP4.......T..............CT
    rs13289550..NR6A1.......A..............................AG
    rs4246586...NRXN1.......G..............................AG
    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
    rs11573443..POLA1.......T..............................CT
    rs4135292...PPARG.......A..AG
    rs28043.....PPIP5K2.....G..............................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
    rs17473.....SERPINA3....G..........................CG
    rs11664907..SERPINB12...G......................AG
    rs36049418..SLC12A3.....A..AG
    rs2328894...SLC17A4.....T..CT
    rs35888596..SLC22A1.....A......................AG
    rs724665....SLC25A40....A..AG
    rs8187643...SLC29A2.....A..............................AC
    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
    rs13067518..STXBP5L.....T..............................CT
    rs4361233...SUSD5.......G..AG
    rs17179194..SYNE2.......A......AG
    rs534564....TAOK3.......A......................AC
    rs16893137..TAPT1.......C..........................CT
    rs2292969...TBCD........C..................CT
    rs3735354...TBXAS1......A..........................AG
    rs526433....TECTA.......G..AG
    rs3093647...TMEM50A.....T..........................CT
    rs5029963...TNFAIP3.....G..................AG
    rs5745989...TNFRSF1B....A......AG
    rs11573970..TNFRSF14....G..........................GG
    rs17722134..TPH2........G..............................AG
    rs12918121..TRADD.......T..............................CT
    rs45498900..TSC2........A......AC
    rs12884433..TSHR........T..CT
    rs12720355..TYK2........G......AG
    rs223469....UBE2D3......T..............................CT
    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
    rs7637797...ZNF501......T..............................CT

    Allyb has rs11191279 on NFKB2 and rs11772720 on ABCB5 shared with GypsyA's daughter (GyD), rs3213102 (missense mutation) on IL12B and rs4988346 on BRIP1 with nandixon, rs11055389 on C12orf36 and rs12554509 (between genes) with ukxmrv, and rs7713754 on AFF4 with Valentijn.
    Waverunner likes this.
  3. GypsyA

    GypsyA

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    I don't really understand a lot of this, but I think if we get enough results we may be able to see some bigger patterns showing up? Thanks for collecting and displaying the information, Valentijn!

    rs10036862 has three of us, so far, with the same mutation. When you were calculating the odds I saw how big a deal it is that something so rare is showing up three times in our group, so far. When my re-test results come back, I'll send them to you. I'm curious if mine will match my daughter's.

    Have any of you had family tested to see what similarities show up?
    Valentijn likes this.
  4. Valentijn

    Valentijn Activity Level: 3

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    Yup!

    We've got a program which is done or nearly done, and makes it much easier, faster, and privater to get results. Basically it's a small program + small database of rare genes that 23andMe tests for which people can download, then they hit two buttons and get a list of their rare genes in about 30 seconds. That can then be easily saved as a text file (tab separated for easy Excel use) or a pdf file (nicer looking for printing).
    GypsyA and ukxmrv like this.
  5. roxie60

    roxie60 Senior Member

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    Valentijn Val I have generated my list and one for my aunt using your new program. I am happy to add mine (and my aunts if you want them but she had a boat load of 1%ers) where I had a more manageable list of around 160 ;). Do you want me to just post mine in this thread?
  6. roxie60

    roxie60 Senior Member

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    Well just went thru the list above and I have some hetero and found one homo minor alelle rs11573970TNFRSF14 GG. So maybe my list a rare ones will add to the overall list? Let me know what you need me to do Val. Looks like Kday and I share this one.


    OK something is not adding up or my brain is not getting 'it'. I just looked for this Rs# on the list of rare genes gened by your program and this gene isn't in the generated list but is on my 23andMe chip. Any ideas? I would think it should show up on the GENEs 0.2 generated list.
  7. Valentijn

    Valentijn Activity Level: 3

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    Does your aunt have ME/CFS too? If so, it'd be cool to see those too. Otherwise it would be great to just see yours, so I can add them to the List.
  8. Valentijn

    Valentijn Activity Level: 3

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    That's a result generated by a different program, and is a mistake - GG is the common version. But basically G isn't rare at all, hence it not being in your results generated by our program. Possibly the other allele should be considered rare, but either 1) it's not quite rare enough to be in the 1% file, or 2) its prevalence hasn't been determined yet by the 1000 genomes project, which is where we got our prevalence data.
    roxie60 likes this.
  9. roxie60

    roxie60 Senior Member

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    Valentijn Wasnt sure where you wanted the list so here it is, can remove it later to make thread less busy if you want.

    SNP GENOTYPE
    rs34248917 CT
    rs7521571 AA
    rs7170 CT
    rs17394875 CT
    rs55896821 AG
    rs1045628 CT
    rs4656345 AG
    rs28384848 CT
    rs17012587 GT
    rs12132342 GT
    rs2715861 CT
    rs2020912 CT
    rs2860771 AG
    rs13428111 AC
    rs17632157 CT
    rs17648863 CT
    rs13027534 AG
    rs17501532 AC
    rs17849638 CT
    rs12993807 AG
    rs17863762 AG
    rs11564445 CT
    rs2317332 AG
    rs3218642 GT
    rs4968 CT
    rs4130 AG
    rs6449181 CT
    rs17880362 CT
    rs11729763 CT
    rs2870750 CT
    rs6413444 AG
    rs308365 CT
    rs17718723 AG
    rs17336381 CT
    rs10519913 CT
    rs10482704 AC
    rs6190 CT
    rs8177425 CT
    rs717925 CG
    rs9501680 AG
    rs17875388 CT
    rs7749944 AC
    rs17180940 GT
    rs3218808 CT
    rs3218816 AG
    rs2254620 AG
    rs35029304 CT
    rs28893563 AG
    rs1704996 AC
    rs11962520 CT
    rs1829212 CT
    rs8180688 CT
    rs11758727 AG
    rs1525745 CT
    rs17883550 CT
    rs28371763 AT
    rs35915664 AG
    rs34589476 CT
    rs1800095 AG
    rs6968076 AC
    rs41725 CT
    rs10503527 CT
    rs7838880 CT
    rs16919296 GT
    rs13279146 AG
    rs11784223 AG
    rs28454876 CT
    rs13290184 GT
    rs28683530 AC
    rs2461180 GT
    rs11596047 AG
    rs4253047 CT
    rs9332235 AG
    rs11572180 AG
    rs17805341 GT
    rs17378597 CT
    rs17883434 AG
    rs57743826 CT
    rs11600966 CT
    rs35329661 CT
    rs36074402 AG
    i3002511 CT
    rs3730071 AC
    rs34102859 AG
    rs7974649 CT
    rs2231696 AG
    rs3730192 CT
    rs10507168 CT
    rs12300729 CC
    rs16942374 AG
    rs11609759 CT
    rs9536258 AG
    rs17220870 CT
    rs17691989 CT
    rs11568438 AG
    rs11570814 AG
    rs17782839 AG
    rs1051193 CT
    rs17778186 AG
    rs17815774 CT
    rs17458021 GT
    rs17190636 CT
    rs1023783 CT
    rs4987018 AC
    rs45474795 GT
    rs11643475 CT
    rs4312323 CT
    rs243848 AG
    rs223870 CT
    rs322581 CT
    rs2232229 AG
    rs17666927 AG
    rs17604185 AC
    rs13329897 CT
    rs201597 AG
    rs11656940 AG
    rs17736841 AG
    rs8178281 AG
    rs2727338 AG
    rs1272340 CT
    rs17648305 CT
    rs16950736 AG
    rs16950754 CT
    i5900811 AG
    rs4987778 AG
    rs4987719 CT
    rs1003467 AC
    rs35303484 AG
    rs1800472 AG
    rs28399654 AG
    rs13045669 AG
    rs13043752 AG
    rs5743497 AG
    rs5613 GT
    rs2792379 TT
    rs17210204 GT
    rs17814116 CT
    rs3970559 AG
    rs34842534 AG
    i5900247 CT
    rs5934953 CT
    rs5906552 AG
    rs5952515 GT
    rs12557243 CT
    rs2207084 AG
    rs10521360 CT
    rs5921615 CT
    rs3093535 CT
    Valentijn likes this.
  10. roxie60

    roxie60 Senior Member

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    i3002511 CT rs1805076
    i5900811 AG rs77960347
    i5900247 CT rs192021326
  11. roxie60

    roxie60 Senior Member

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    Finding that is curious, would others check ABCC4 in SNPedia and goto bottom right, check the 10 SNPs listed (8 in my case). I am curious, all 8 of mine were homozygous, and I so far have four more homozyg ones based on Val's program. I just want to know if this is an anomaly or if everyone is seeing homozyg for all the ABCC4 SNPs, thx.
  12. roxie60

    roxie60 Senior Member

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  13. roxie60

    roxie60 Senior Member

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    another more specific Pharma list

    something I just noticed on this, if you have the Firefox plug-in for SNPs this list will show some Rs#'s in red, appearing to signify at a glace which once you are homozyg and possibly at risk (I have not had chance to verify this yet). Could help one focus on just the red one's and verify your gene status and potential drug metabolism status. UPDATE: Just found my observation not true, although majority of Rs#s in red were homozyg, I found two that were hetero so I still not sure the relavance of the Rs#'s in red). UPDATE2: I think I figured it out, the Rs#'s in red appear ti indicate SNPedia has not information in these as yet.

    SNPs on this page are known to influence absorption, distribution, metabolism, and excretion

    http://www.snpedia.com/index.php/Pharma_ADME
  14. Valentijn

    Valentijn Activity Level: 3

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    Something that can happen is that basically everyone inherits a certain bunch of SNPs as a clump which always stays together. So it's not always more significant to have two (or five, or ten) rare SNPs on a gene compared to just having one rare SNP on that gene.

    Looking at the prevalence data can help figure that out - if it's exactly the same for each SNP, then it's probably just a clump. But if it's fairly different for SNPs, then the additional ones could still be significant.
  15. Valentijn

    Valentijn Activity Level: 3

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    There's a new version of the program to download. Functionally identical to the old ones, but it now checks to make sure a proper and unzipped rare genes database has been selected.

    And if someone tries to run the zipped version of the program, it will work now but without the comments added (such as additional RS numbers, but homozygous results will still get flagged). Much better to just unzip everything!

    Please let me know if there's still anyone having problems.
    ukxmrv likes this.
  16. Sea

    Sea Senior Member

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    I am hetero for 3 of those 8 snps and have the major alleles for the other 5

    Out of the 564 snps tested on that gene by 23andme I have
    11 no call
    112 heterozygous
    Don't know about homozygous without checking individually.

    I wish 23andme would show with our results which ones are polymorphisms. Heteros are easy to spot
    roxie60 likes this.
  17. roxie60

    roxie60 Senior Member

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    ok so one of my very rare SNPs (<1%) for POLR3B is CC (risk alelle). Research indicates POLR3B gene; 'C' rare/risk alelle; Mutations in this gene are a cause of hypomyelinating leukodystrophy.

    from wiki : Leukodystrophy refers to a group of disorders characterized by degeneration of the white matter in the brain.[1] The leukodystrophies are caused by imperfect growth or development of the myelin sheath, the fatty covering that acts as an insulator around nerve fibers. Myelin in the CNS is produced by oligodendrocytes.[2] When damage occurs to white matter tissue immune responses can lead to inflamation in the CNS, along with loss of myelin.

    So my question is, I have the rare genetic variant for this condition and yet I'm not aware that I have. So what can we really conclude from our 23andME data when we now we are homozyg for the risk alelle and yet we do not appear to have the condition identified? Th only thing I was told in January was I had white spots on my brain but dr said due to migraines that I have 4-5 times a year....

    A little more on POLR3B from NIH
    The protein encoded by this gene is the catalytic component of RNA polymerase III, which synthesizes small RNAs. The encoded protein also acts as a sensor to detect foreign DNA and trigger an innate immune response.


    Well I do seem to have a boat load of immune responses o_O

    http://ghr.nlm.nih.gov/condition/pol-iii-related-leukodystrophy
  18. wordweaver27

    wordweaver27

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    I've run my raw data through the Rare Alleles program and find it fascinating. Valentijn, Would you like to add it to the list? If so, shall I PM it to you (lmk what format-excel or text) or post here?
    THanks :)
  19. GypsyA

    GypsyA

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    roxie60, from what I understand we can have the mutations, but they aren't doing any damage unless those mutated cells are turned on. Maybe I didn't understand it correctly, though? I have suffered from a lifetime of migraines, as did my own mother who died early (from cervical cancer). EEK! My brain must be mostly white by now if you have white spots from migraines only 4-5 times a year.

    For the myelin sheath, I'm fairly certain I have issues with that. I have CFS and Lyme...and in the beginning when I was in excruciating pain for nearly a year a lovely scientist recommended that I take a tablespoon of ghee per day to help with the issue, and WOW! Within three days the pain I'd suffered with for an entire year disappeared. Since that time my body has been struggling with many other issues which result in pain, so the ghee doesn't work as beautifully now as it did in the past. I'm pretty sure I came across information that hemp oil will help with the myelin sheath, also.

    I'm looking forward to reading more responses for your question. I practically live on this board, lurking and learning.
    merylg and roxie60 like this.
  20. bel canto

    bel canto Senior Member

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    Roxie - isn't it possible that you have genetics that partly or mostly compensate for the impaired one? I know that seems to be the case for various autoimmune disease susceptibilities.

    It seems that these rare alleles might be useful to us only if they were to make sense based on our symptoms, and be a clue to a way to get a bit better.

    I don't know about you, but I'm quite frustrated with trying to figure out which ones are possibly significant, or even what a lot of them do. SNPedia often doesn't have any information, and the genetic databases are often just incomprehensible to those of us without the science background.

    Hopefully, we can share our research on any alleles that we share. And maybe some biochemist will take pity on us and give us a few insights.

    Val - thanks again for all your effort to do this program!
    merylg, Valentijn and roxie60 like this.

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