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1 Reference Sequence Number Gene Symbol Alleles Chromosomal

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1 Reference Sequence Number Gene Symbol Alleles Chromosomal 1 Supplemental Table 1. 10,177 non-synonymous single nucleotide polymorphisms on ParAllele panel; the San Francisco Bay Area Adult Glioma Study Minor Allele Minor Allele Reference Sequence Chromosomal Frequency, Frequency, Number Gene Symbol Alleles Location Minor Allele Case Control P-value* rs8289 FUT6, M6PRBP1 A/G 19p A 0.357798165 0.188073394 0.000141 rs10495960 LHCGR, GTF2A1L A/G 02p A 0.102678571 0.245454545 0.000145 rs1195889 GPR133 A/G 12q A 0.339285714 0.495495495 0.000547 rs11076585 C/T 16q T 0.147321429 0.290178571 0.00055 rs10415562 OR7C1 C/T 19p C 0.294642857 0.183035714 0.000805 rs7955866 FGF23 A/G 12p A 0.163636364 0.049549549 0.001078 rs3765083 MFSD1 A/G 03q A 0.486607143 0.339285714 0.001137 rs12455859 G/T 18p G 0.473214286 0.366071429 0.001248 rs3732548 hCG_1813818 A/C 03p C 0.21875 0.357142857 0.001609 rs1047840 EXO1 A/G 01q A 0.321428571 0.468181818 0.002261 rs10817025 SVEP1 C/T 09q C 0.403061224 0.252747253 0.002461 rs1265054 C6orf15 A/G 06p A 0.382882883 0.468468468 0.002688 rs319522 GPC6 A/G 13q G 0.40625 0.455357143 0.003242 rs7522157 CLCC1, C1orf62 C/T 01p T 0.254464286 0.382882883 0.003275 rs2017467 A/G 11q A 0.068181818 0.155963303 0.003282 rs4272850 TMEM132C A/G 12q A 0.294642857 0.178571429 0.003348 rs10490923 ARMS2 A/G 10q A 0.09375 0.196428571 0.003436 rs1129770 CMYA5 A/G 05q A 0.142857143 0.258928571 0.003448 rs2298771 SCN1A A/G 02q G 0.361607143 0.232142857 0.003505 rs6902416 TRDN C/G 06q G 0.1875 0.09009009 0.004266 rs2502601 SYNJ2 C/T 06q T 0.40625 0.459821429 0.0043 rs4691212 G/T 04q G 0.267857143 0.392857143 0.004421 rs3734960 DPP6 C/T 07q C 0.34375 0.218181818 0.004809 rs3817121 CAND2 A/G 03p A 0.245535714 0.138392857 0.005011 rs12610412 ZNF77 C/G 19p G 0.169642857 0.080357143 0.005096 rs2296308 RWDD3 G/T 01p T 0.171171171 0.081081081 0.005159 rs266881 KLK3 A/C 19q A 0.440366973 0.41588785 0.005503 rs1046116 PKP2 C/T 12p C 0.27027027 0.160714286 0.005733 rs2747701 FAM135A A/G 06q A 0.433035714 0.441441441 0.006122 rs4801958 ZNF665 C/T 19q C 0.455357143 0.328828829 0.006323 rs3177253 PECI A/G 06p A 0.223214286 0.339285714 0.006341 rs6949654 tcag7.1314 C/T 07q T 0.178571429 0.089285714 0.006551 Page 1 1 rs3803704 FLJ11171 A/G 16q G 0.321428571 0.205357143 0.006644 rs7022771 A/C 09q A 0.291262136 0.41509434 0.006828 rs10911825 HMCN1 A/G 01q G 0.325892857 0.214285714 0.006939 rs12360890 OR5T1 A/G 11q G 0.459821429 0.325892857 0.007113 rs843971 PGLYRP3 A/G 01q A 0.297297297 0.419642857 0.007251 rs1265053 C6orf15 C/G 06p C 0.341121495 0.476635514 0.007562 rs1657133 A/G 16p G 0.133027523 0.229357798 0.007829 rs10845293 TAS2R44 A/G 12p A 0.416666667 0.462616822 0.007847 rs709564 CCDC54 A/G 03q A 0.196428571 0.299107143 0.008181 rs799661 A/G 14q A 0.068807339 0.138392857 0.008647 rs2862954 ERLIN1 C/T 10q T 0.397321429 0.473214286 0.008824 rs12460170 ZNF665 A/G 19q A 0.45045045 0.330357143 0.009014 rs10896271 OR8K1 A/G 11q G 0.455357143 0.325892857 0.009332 rs998544 OR5R1 C/T 11q T 0.455357143 0.325892857 0.009332 rs511987 A/G 11q G 0.446428571 0.321428571 0.009383 rs10028124 SCLT1 A/T 04q T 0.397321429 0.279279279 0.009603 rs1742429 C16orf73 C/T 16p C 0.126126126 0.21875 0.009638 rs8097835 A/G 18q A 0.383928571 0.490990991 0.009657 rs7226913 OSBPL1A C/T 18q C 0.40625 0.473214286 0.009687 rs3123101 VIL2, SYTL3 A/T 06q T 0.325892857 0.214285714 0.009707 rs1421217 C/T 08q C 0.482142857 0.396396396 0.009864 rs7000148 C8orf68 C/G 08p C 0.415178571 0.290178571 0.009871 rs6235 PCSK1 C/G 05q C 0.223214286 0.339285714 0.01003 rs4590080 LIMCH1 C/G 04p C 0.072072072 0.013513513 0.010241 rs2014576 SIX5 C/T 19q C 0.387387387 0.490990991 0.010394 rs911391 A/C 16p A 0.133027523 0.227678571 0.010747 rs1056320 MGC24039 A/C 12p A 0.160714286 0.075892857 0.010755 rs2022923 MGC39715 A/G 08q G 0.355855856 0.472972973 0.010953 rs3783941 TSHR G/T 14q G 0.400900901 0.285714286 0.011044 rs10888390 CTSS A/G 01q A 0.303571429 0.424107143 0.011053 rs2242373 FLJ35773 C/T 17p T 0.125 0.214285714 0.011096 rs4555873 C/T 05q T 0.378378378 0.258928571 0.011157 rs3118574 A/G 09q A 0.272321429 0.382882883 0.01122 rs3806692 LOC401068 C/G 03p C 0.129464286 0.058035714 0.011288 rs9639168 ETV1 C/T 07p C 0.294642857 0.410714286 0.01153 rs12115750 LOC402377 A/C 09q A 0.085585586 0.160714286 0.011651 rs1935 JMJD1C C/G 10q G 0.436936937 0.449074074 0.011651 Page 2 1 rs2458236 DUOX1 C/T 15q C 0.413636364 0.296296296 0.012023 rs2898904 A/G 11p G 0.439814815 0.327102804 0.012136 rs5748648 XKR3 A/G 22q A 0.107142857 0.045045045 0.012189 rs12096753 TRIM67 C/T 01q C 0.111607143 0.205357143 0.012308 rs3813636 C1orf49 G/T 01q G 0.469072165 0.403061224 0.012503 rs649058 TNNI3K A/G 01p G 0.491071429 0.397321429 0.012544 rs9806945 C16orf73 A/G 16p G 0.131818182 0.223214286 0.01258 rs1553316 HAVCR1 C/T 05q T 0.09375 0.174107143 0.01259 rs2285374 A/G 11q G 0.450892857 0.333333333 0.012642 rs8030587 STARD9 A/G 15q A 0.265765766 0.169642857 0.012652 rs1291212 ZGPAT C/G 20q C 0.09009009 0.032110092 0.012993 rs1006954 ZZEF1 C/T 17p T 0.081081081 0.15625 0.013052 rs10825269 PCDH15 C/T 10q T 0.080357143 0.15625 0.013123 rs10022054 LOC402175 A/G 04p G 0.125 0.053571429 0.013395 rs8023524 CDAN1 A/G 15q A 0.235576923 0.136792453 0.013523 rs2045571 FCGR2B C/T 01q T 0.089622642 0.164948454 0.013544 rs560389 A/G 01p A 0.263392857 0.370535714 0.013678 rs12568310 FLJ35530 C/T 01q T 0.446428571 0.333333333 0.013762 rs2274756 MMP9 A/G 20q A 0.116071429 0.202702703 0.013772 rs9532758 MTRF1 C/T 13q C 0.108108108 0.040178571 0.013823 rs1065838 C16orf45 C/T 16p C 0.316513761 0.213636364 0.013829 rs2637777 FAT G/T 04q G 0.325892857 0.446428571 0.01394 rs10904481 UCN3 A/G 10p G 0.370535714 0.261261261 0.014251 rs1381657 CENPE C/G 04q G 0.217592593 0.135135135 0.014263 rs6234 PCSK1 C/G 05q G 0.225225225 0.336363636 0.014507 rs10817479 WDR31 A/G 09q A 0.095454545 0.036036036 0.014973 rs2306595 MYOHD1 C/T 17q C 0.086363636 0.03125 0.015081 rs2306175 C4orf26 A/G 04q A 0.169642857 0.263392857 0.015123 rs227787 OR3A3 C/T 17p C 0.205357143 0.301801802 0.015262 rs1801516 ATM A/G 11q A 0.098214286 0.183035714 0.015312 rs2208525 G/T 20q T 0.207207207 0.303571429 0.015664 rs2280544 BET1L C/T 11p T 0.207207207 0.303571429 0.015678 rs6983981 C8orf68 A/C 08p C 0.387387387 0.272321429 0.015777 rs3213831 PZP C/T 12p T 0.385321101 0.5 0.01587 rs12568050 ZNF648 C/G 01q C 0.189189189 0.110091743 0.016023 rs4245199 PVRL1 G/T 11q G 0.117117117 0.054545454 0.016052 rs710187 GCAT C/T 22q C 0.482142857 0.403669725 0.016496 Page 3 1 rs10836399 OR51D1 C/G 11p C 0.165178571 0.258928571 0.016558 rs11230600 OR4C6 C/T 11q C 0.339285714 0.232142857 0.016685 rs1459101 OR4C16 A/G 11q A 0.339285714 0.232142857 0.016685 rs4987236 A/G 08p A 0.072072072 0.022522522 0.016757 rs7811042 CCDC129 A/C 07p C 0.368686869 0.260869565 0.016823 rs2266988 PRAME A/G 22q A 0.352678571 0.464285714 0.016995 rs2280205 SLC2A9 A/G 04p G 0.49537037 0.390909091 0.017326 rs3823430 DNAH8 C/T 06p C 0.111607143 0.191964286 0.017409 rs10816 C13orf28 A/T 13q A 0.45045045 0.342342342 0.017653 rs1051624 CDH17 A/C 08q A 0.473214286 0.405405405 0.01772 rs3817672 TFRC A/G 03q G 0.5 0.391891892 0.017722 rs1805127 KCNE1 A/G 21q A 0.308035714 0.419642857 0.017774 rs9850805 A/C 03q A 0.252252252 0.36036036 0.018056 rs627933 C/T 11q C 0.245535714 0.351351351 0.018572 rs4949211 C/T 01p C 0.477272727 0.405660377 0.019046 rs3798130 KIF3A A/G 05q A 0.118181818 0.200892857 0.019145 rs447802 FAM83E C/T 19q C 0.211711712 0.304545454 0.019167 rs2372536 ATIC C/G 02q G 0.267857143 0.375 0.019415 rs626251 C1orf87 C/T 01p C 0.364864865 0.482142857 0.019488 rs4902695 C/T 14q T 0.223214286 0.321428571 0.019609 rs1151625 LIME1, SLC2A4RG C/T 20q T 0.089285714 0.035714286 0.019707 rs9394866 FLJ90086 A/G 06p G 0.459821429 0.433035714 0.020243 rs3733242 SHROOM3 A/G 04q A 0.357142857 0.46875 0.020391 rs966365 EDARADD C/T 01q C 0.133928571 0.214285714 0.020476 rs10851704 VPS13C C/T 15q T 0.424107143 0.463963964 0.020719 rs2074469 OR10C1 A/G 06p G 0.165178571 0.254464286 0.020745 rs10076911 FLJ13231 A/C 05p C 0.160714286 0.089285714 0.020984 rs648614 TNNI3K C/T 01p C 0.477678571 0.418918919 0.021553 rs2609881 ZNF228 A/C 19q C 0.085585586 0.160714286 0.021965 rs10078391 DNAH5 C/T 05p C 0.160714286 0.245535714 0.022032 rs365990 MYH6 A/G 14q G 0.330357143 0.436363636 0.022069 rs6428538 A/G 01p A 0.071428571 0.138392857 0.022254 rs2799123 C/G 09p G 0.400900901 0.292792793 0.022384 rs2799125 C/T 09p T 0.401785714 0.294642857 0.022399 rs10146482 NEK9 C/T 14q T 0.472972973 0.414414414 0.023071 rs2836662 C21orf24 A/T 21q A 0.279279279 0.376146789 0.023109 rs2276976 NHEDC2 A/C 04q C 0.133928571 0.071428571 0.023197 Page 4 1 rs11230864 C/T 11q T 0.454954955 0.34375 0.023216 rs2293172 GIMAP4 A/C 07q A 0.116071429 0.189189189 0.02336 rs10017772 DCHS2 C/T 04q C 0.459821429 0.433035714 0.023585 rs7032785 JAK2 C/T 09p C 0.4375 0.454954955 0.023589 rs9616310 C/G 22q G 0.330357143 0.433035714 0.023786 rs11024970 MRGPRX2 G/T 11p G 0.080357143 0.03125 0.02381 rs1110627 DLL3 A/G 19q A 0.446428571 0.446428571 0.0247 rs376618 FGFR4 A/G 05q G 0.308411215 0.213636364 0.024724 rs2231926 FLJ10213, PPP4R2 A/G 03p A 0.495454546 0.391891892 0.024789 rs3823603 IQCE C/G 07p C 0.222727273 0.325892857 0.024807 rs2486668 GRHL3 C/G 01p C 0.198198198 0.117117117 0.024937 rs10408247 CEACAM20 A/G 19q A 0.142857143 0.075892857 0.025046 rs3741845 TAS2R9 C/T 12p T 0.444444444 0.341584158 0.02512 rs2748404 FLJ43860 G/T 08q G 0.261261261 0.352678571 0.025268 rs7157977 C/T 14q T 0.352678571 0.450450451 0.025358 rs10120210 ECM2, CENPP G/T 09q T 0.481818182 0.372727273 0.025503 rs11568658 ABCC4 G/T 13q T
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