Rare allele data

[Valentijn]

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 ) 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

 

[Valentijn]

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.

 

[GypsyA]

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]

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?

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).

 

[roxie60]

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?

 

[roxie60]

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.

 

[Valentijn]

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?

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.

 

[Valentijn]

Well just went thru the list above and I have some hetero and found one homo minor alelle rs11573970 TNFRSF14 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.

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]

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

 

[roxie60]

i3002511 CT rs1805076
i5900811 AG rs77960347
i5900247 CT rs192021326

 

[roxie60]

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.

 

[roxie60]

Not sure best use for this yet, sharing justin case someone figures out how best to use.

Pharma DMET list of SNPs and genes

http://www.snpedia.com/index.php/Pharma_DMET

 

[roxie60]

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

 

[Valentijn]

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.

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.

 

[Valentijn]

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.

 

[Sea]

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.

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]

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

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

 

[wordweaver27]

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

 

[GypsyA]

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.

 

[bel canto]

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!