Table A2.
Information About 100 Top Ranking Glioma Susceptibility SNPs From Our Previous Glioma GWAS
| SNP | Chr | Gene | Base Change | MAF |
Log-Rank P | χ2 Test P |
|||
|---|---|---|---|---|---|---|---|---|---|
| NCBI | MDACC Cases | Codominant | Dominant | Recessive | |||||
| rs13099725 | 3 | C3orf56 | A/G | 0.15 | 0.15 | .002 | .043 | .35 | .032 |
| rs4734443 | 8 | RGS22 | C/T | 0.458 | 0.38 | .003 | .067 | .87 | .033 |
| rs7325927 | 13 | LIG4 | C/T | 0.225 | 0.29 | .008 | .027 | .004 | .052 |
| rs11670188 | 19 | BTBD2 | A/G | 0.217 | 0.23 | .009 | .036 | .02 | .25 |
| rs2297440 | 20 | RTEL1 | C/T | 0.258 | 0.18 | .02 | .038 | .024 | .083 |
| rs6010620 | 20 | RTEL1 | A/G | 0.258 | 0.19 | .021 | .051 | .041 | .17 |
| rs1380994 | 8 | RGS22 | A/G | 0.467 | 0.39 | .038 | .077 | 1 | .033 |
| rs9656979 | 8 | CCDC26 | C/T | 0.407 | 0.45 | .0381 | .05 | .23 | .12 |
| rs10131032 | 14 | AKAP6 | A/G | 0.108 | 0.08 | .0435 | .13 | .14 | .079 |
| rs2781321 | 1 | DAB1 | A/G | 0.458 | 0.47 | .0632 | .57 | .31 | .91 |
| rs10924559 | 1 | SMYD3 | A/G | 0.044 | 0.16 | .0671 | .64 | .56 | .53 |
| rs2094354 | 13 | LOC644623 | A/G | 0.125 | 0.07 | .069 | .41 | .8 | .21 |
| rs1509937 | 10 | CTNNA3 | A/G | 0.383 | 0.36 | .1006 | .073 | .49 | .065 |
| rs2110922 | 2 | SLC8A1 | G/T | 0.392 | 0.39 | .1028 | .09 | .091 | .03 |
| rs9514044 | 13 | C13orf39 | C/T | 0.175 | 0.27 | .113 | .27 | .16 | .24 |
| rs10464870 | 8 | CCDC26 | C/T | 0.175 | 0.23 | .1137 | .018 | .011 | .017 |
| rs6765837 | 3 | VPS8 | C/T | 0.467 | 0.46 | .121 | .046 | .025 | .79 |
| rs17745484 | 2 | DNMT3A | C/T | 0.325 | 0.36 | .1422 | .12 | .076 | .61 |
| rs1563834 | 12 | HMGA2 | A/G | 0.102 | 0.14 | .1462 | .056 | .045 | .027 |
| rs3770876 | 2 | CRIM1 | A/C | 0.353 | 0.45 | .1662 | .045 | .041 | .054 |
| rs200888 | 20 | PTPNS1 | G/T | 0.417 | 0.41 | .1785 | .4 | .22 | .36 |
| rs13268364 | 8 | PEBP4 | C/T | 0.267 | 0.28 | .1876 | .019 | .13 | .052 |
| rs1681655 | 3 | TBL1XR1 | C/T | 0.133 | 0.09 | .1922 | .015 | .22 | .31 |
| rs171125 | 16 | TP53TG3 | A/G | 0.147 | 0.11 | .2603 | .26 | .24 | .21 |
| rs7513553 | 1 | PPT1 | G/T | 0.186 | 0.21 | .2626 | .2 | .075 | .49 |
| rs7282227 | 21 | C21orf37 | C/T | 0.075 | 0.07 | .2658 | .19 | .14 | .38 |
| rs7849795 | 9 | C9orf123 | G/T | 0.259 | 0.2 | .3161 | .17 | .56 | .06 |
| rs1340949 | 10 | LOC220929 | C/T | 0.475 | 0.42 | .3192 | .28 | .54 | .24 |
| rs9922943 | 16 | SLC38A8 | C/T | 0.15 | 0.2 | .3271 | .5 | .62 | .24 |
| rs891835 | 8 | CCDC26 | G/T | 0.175 | 0.24 | .3308 | .011 | .024 | .013 |
| rs10229692 | 7 | CNTNAP2 | A/G | 0.059 | 0.09 | .3327 | .46 | .62 | .22 |
| rs10149208 | 14 | LOC729646 | A/G | 0.435 | 0.38 | .335 | .73 | .45 | 1 |
| rs6931798 | 6 | LRFN2 | C/T | 0.138 | 0.22 | .3541 | .76 | .47 | .75 |
| rs12033655 | 1 | DAB1 | C/T | 0.375 | 0.27 | .3578 | .49 | .83 | .24 |
| rs13023983 | 2 | FIGN | A/C | 0.142 | 0.24 | .3706 | .94 | .79 | .78 |
| rs999051 | 1 | PRELP | C/T | 0.169 | 0.12 | .3752 | .5 | .24 | .72 |
| rs2206920 | 20 | BMP2 | A/G | 0.085 | 0.1 | .3777 | .35 | .17 | .96 |
| rs7124728 | 11 | LOC220070 | C/T | 0.362 | 0.36 | .3818 | .52 | .93 | .27 |
| rs17748 | 11 | TREH | C/T | 0.233 | 0.23 | .3869 | .63 | .39 | .53 |
| rs9369226 | 6 | LRFN2 | A/G | 0.161 | 0.23 | .388 | .81 | .53 | .75 |
| rs4980684 | 11 | FGF19 | C/T | 0.408 | 0.41 | .4464 | .79 | .7 | .51 |
| rs1941114 | 18 | CHST9 | A/G | 0.158 | 0.13 | .4598 | .24 | .44 | .2 |
| rs2853676 | 5 | TERT | A/G | 0.275 | 0.33 | .474 | .11 | .063 | .15 |
| rs6914611 | 6 | PREP | C/T | 0.1 | 0.08 | .4856 | .36 | .32 | .19 |
| rs6869535 | 5 | PTGER4 | A/G | 0.142 | 0.13 | .5073 | .65 | .64 | .37 |
| rs8127220 | 21 | C21orf37 | A/G | 0.067 | 0.06 | .5249 | .36 | .32 | .38 |
| rs7562790 | 2 | CRIM1 | G/T | 0.358 | 0.45 | .542 | .043 | .042 | .061 |
| rs7219550 | 17 | POLR2A | A/G | 0.149 | 0.18 | .561 | .35 | .2 | .78 |
| rs7257116 | 19 | MKNK2 | C/T | 0.317 | 0.35 | .5779 | .68 | .38 | .7 |
| rs4490127 | 2 | COL6A3 | G/T | 0.5 | 0.45 | .5914 | .079 | .028 | .81 |
| rs10771012 | 12 | SOX5 | A/G | 0.475 | 0.47 | .5922 | 1 | .99 | .97 |
| rs1789374 | 11 | RDX | C/T | 0.263 | 0.33 | .5969 | .96 | .83 | .8 |
| rs11727564 | 4 | ANP32C | G/T | 0.308 | 0.29 | .6089 | .28 | .29 | .15 |
| rs2224601 | 9 | C9orf123 | A/G | 0.237 | 0.19 | .614 | .57 | .68 | .3 |
| rs2208742 | 9 | C9orf123 | C/T | 0.242 | 0.19 | .614 | .57 | .68 | .3 |
| rs10197919 | 2 | FBLN7 | A/G | 0.441 | 0.44 | .6147 | .74 | .51 | .91 |
| rs1063192 | 9 | CDKN2A/B | C/T | 0.4 | 0.49 | .6193 | .73 | .47 | .57 |
| rs727675 | 14 | HECTD1 | A/G | 0.475 | 0.46 | .6268 | .91 | .7 | .95 |
| rs4977756 | 9 | CDKN2A/B | A/G | 0.342 | 0.46 | .6423 | .49 | .3 | .35 |
| rs6042018 | 20 | FKBP1A | C/T | 0.425 | 0.32 | .6454 | .61 | .91 | .33 |
| rs4837334 | 9 | SH3GLB2 | A/G | 0.317 | 0.3 | .6527 | .59 | .74 | .41 |
| rs6761 | 17 | POLR2A | C/T | 0.392 | 0.4 | .6562 | .83 | .99 | .56 |
| rs2180273 | 1 | TRIM67 | C/T | 0.178 | 0.2 | .669 | .43 | .56 | .22 |
| rs833141 | 2 | PDE1A | G/T | 0.108 | 0.11 | .675 | .45 | .71 | .21 |
| rs3853894 | 17 | ZBTB4 | A/G | 0.5 | 0.16 | .694 | .55 | .28 | .64 |
| rs1384847 | 4 | RASL11B | A/G | 0.067 | 0.06 | .6975 | .71 | .76 | .41 |
| rs1079950 | 6 | PARK2 | A/G | 0.277 | 0.37 | .7238 | .49 | .29 | .41 |
| rs7594432 | 2 | DNMT3A | C/T | 0.383 | 0.39 | .7306 | .76 | .55 | .55 |
| rs11682175 | 2 | VRK2 | C/T | 0.425 | 0.43 | .7381 | .89 | .68 | .71 |
| rs870283 | 1 | CAMTA1 | C/T | 0.442 | 0.35 | .75 | .7 | .78 | .39 |
| rs3748699 | 1 | UCK2 | A/G | 0.133 | 0.12 | .755 | .088 | .12 | .075 |
| rs16852868 | 1 | UCK2 | A/C | 0.129 | 0.12 | .758 | .088 | .12 | .075 |
| rs10082804 | 12 | FLJ23560 | C/T | 0.085 | 0.16 | .7625 | .32 | .22 | .53 |
| rs10488631 | 7 | TNPO3 | C/T | 0.167 | 0.11 | .7687 | .95 | .76 | .97 |
| rs12531711 | 7 | TNPO3 | A/G | 0.167 | 0.11 | .7687 | .95 | .76 | .97 |
| rs7862315 | 9 | USP20 | A/G | 0.088 | 0.13 | .7837 | .78 | .5 | .96 |
| rs9901643 | 17 | POLR2A | A/G | 0.15 | 0.16 | .7938 | .58 | .48 | .61 |
| rs1998027 | 1 | TRIM67 | A/G | 0.32 | 0.46 | .7943 | .36 | .18 | .97 |
| rs10170021 | 2 | BBS5 | C/T | 0.217 | 0.31 | .7967 | .57 | .55 | .3 |
| rs498872 | 11 | PHLDB1 | C/T | 0.325 | 0.33 | .8101 | .79 | .96 | .52 |
| rs1484874 | 18 | SLC14A2 | A/G | 0.392 | 0.44 | .8147 | .95 | .91 | .79 |
| rs2157719 | 9 | CDKN2A/B | A/G | 0.383 | 0.48 | .8165 | .54 | .28 | .92 |
| rs16904140 | 8 | CCDC26 | A/G | 0.158 | 0.23 | .8389 | .37 | .35 | .2 |
| rs6662747 | 1 | CAMTA1 | A/G | 0.48 | 0.42 | .8448 | .84 | .97 | .57 |
| rs11887120 | 2 | DNMT3A | C/T | 0.356 | 0.37 | .8568 | .57 | .88 | .3 |
| rs9526689 | 13 | DLEU7 | A/G | 0.058 | 0.05 | .8623 | .7 | .85 | .50 |
| rs4295627 | 8 | CCDC26 | G/T | 0.142 | 0.2 | .8643 | .49 | .28 | .45 |
| rs2678919 | 2 | VRK2 | A/G | 0.258 | 0.25 | .865 | .64 | .68 | .46 |
| rs7325443 | 13 | LIG4 | C/T | 0.17 | 0.22 | .9011 | .27 | .33 | .3 |
| rs265120 | 1 | GPATCH2 | C/T | 0.102 | 0.15 | .9162 | .82 | .57 | .72 |
| rs4738442 | 8 | JPH1 | C/T | 0.075 | 0.03 | .9236 | .69 | .67 | .49 |
| rs7300686 | 12 | TMEM132C | C/T | 0.457 | 0.41 | .9255 | .41 | .77 | .19 |
| rs9959776 | 18 | LOC728662 | G/T | 0.358 | 0.45 | .9295 | .98 | .93 | .91 |
| rs6470745 | 8 | CCDC26 | A/G | 0.142 | 0.22 | .9459 | .8 | .55 | .92 |
| rs2243988 | 21 | RUNX1 | C/T | 0.331 | 0.38 | .9521 | .75 | .56 | .8 |
| rs1412829 | 9 | CDKN2A/B | C/T | 0.367 | 0.47 | .9671 | .68 | .44 | .92 |
| rs6092361 | 20 | TFAP2C | C/G | 0.191 | 0.38 | .9793 | .93 | .8 | .71 |
| rs2736100 | 5 | TERT | G/T | 0.45 | 0.41 | .9916 | .85 | .58 | .8 |
| rs927704 | 14 | HECTD1 | A/C | 0.425 | 0.44 | .9958 | .96 | .87 | .86 |
| rs2072532 | 2 | SLC8A1 | C/T | 0.458 | 0.43 | .1120 | .058 | .022 | .15 |
Abbreviations: SNP, single nucleotide polymorphism; GWAS, genome-wide association study; Chr, chromosome; MAF, minor allele frequency; NCBI, National Center for Biotechnology Information; MDACC, M. D. Anderson Cancer Center.
*
MAF for CEU in the NCBI dbSNPs database.
†
Log-rank test P value for overall survival.
‡
P value for difference in genotype distributions between long-term survivors and short-term survivors.