Table 1.
Summary of GWAS-reported genetic loci associated with glioma risk
| Author (year) | Ancestry | Type | SNP | Locus | Nearby gene | Annotationa | Alleleb | EAFc | P d | ORGWASe | P GWAS e | PMIDf |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Melin (2017) | White | GBM | rs12752552 | 1p31.3 | RAVER2 | Intronic | T/C | 1.00/0.87 | 2.18E-32 | 1.22 | 2.04E-09 | 28346443 |
| Melin (2017) | White | Non-GBM | rs4252707 | 1q32.1 | MDM4 | Intronic | A/G | 0.40/0.22 | 1.06E-18 | 1.19 | 3.34E-09 | 28346443 |
| Melin (2017) | White | Non-GBM | rs12076373 | 1q44 | AKT3 | Intronic | G/C | 0.68/0.84 | 7.38E-16 | 1.23 | 2.63E-10 | 28346443 |
| Melin (2017) | White | Non-GBM | rs7572263 | 2q33.3 | C2orf80 | Intronic | A/G | 0.97/0.76 | 2.05E-45 | 1.20 | 2.18E-10 | 28346443 |
| Eckel-Passow (2020) | White | IDH mutation | rs5839764 | 2q37.3 | D2HGDH | Intronic | G/C | 0.41/0.38 | 0.215 | 1.51/1.56 | 2.82E-10 | 32386320 |
| Eckel-Passow (2020) | White | IDH mutation and 1p/19q non-codeletion | rs1106639 | 2q37.3 | D2HGDH | Missense | A/G | 0.12/0.26 | 2.82E-15 | 1.71/1.72 | 4.96E-08 | 32386320 |
| Melin (2017) | White | Non-GBM | rs11706832 | 3p14.1 | LRIG1 | Intronic | C/A | 0.19/0.46 | 6.02E-37 | 1.15 | 7.66E-09 | 28346443 |
| Walsh (2014) | White | GBM | rs1920116 | 3q26.2 | LRRC31 | Intronic | G/A | 0.39/0.71 | 1.90E-47 | 1.30 | 8.30E-09 | 24908248 |
| Shete (2009) | White | Overall | rs2736100 | 5p15.33 | TERT | Intronic | G/T | 0.41/0.50 | 1.46E-04 | 1.27 | 1.50E-17 | 19578367 |
| Chen (2019) | East Asian | Overall | rs2736100 | 5p15.33 | TERT | Intronic | G/T | 0.41/0.50 | 1.46E-04 | 1.27 | 2.45E-12 | 30714141 |
| Eckel-Passow (2020) | White | Triple-positive | rs111976262 | 7p22.3 | FAM20C | Intergenic | A/C | 0.01/0.04 | 6.55E-05 | 3.52/3.05 | 9.56E-09 | 32386320 |
| Sanson (2011) | White | Overall | rs11979158 | 7p11.2 | EGFR | Intronic | A/G | 1.00/0.83 | 5.41E-41 | 1.23 | 7.72E-08 | 21531791 |
| Sanson (2011) | White | Overall | rs2252586 | 7p11.2 | EGFR | Intergenic | T/C | 0.02/0.28 | 3.94E-61 | 1.18 | 2.09E-08 | 21531791 |
| Jenkins (2012) | White | Overall | rs55705857 | 8q24.21 | CCDC26 | Intergenic | G/A | 0.00/0.06 | 1.77E-14 | 3.11 | 5.00E-25 | 22922872 |
| Shete (2009) | White | Overall | rs4295627 | 8q24.21 | CCDC26 | Intergenic | G/T | 0.23/0.18 | 4.99E-03 | 1.36 | 2.34E-18 | 19578367 |
| Shete (2009) | White | Overall | rs4977756 | 9p21.3 | CDKN2B-AS1 | Intronic | G/A | 0.21/0.40 | 2.31E-21 | 1.24 | 7.24E-15 | 19578367 |
| Melin (2017) | White | Non-GBM | rs11598018 | 10q24.33 | OBFC1 | Intronic | C/A | 0.66/0.46 | 6.45E-19 | 1.14 | 3.39E-08 | 28346443 |
| Kinnersley (2015) | White | Non-GBM | rs11196067 | 10q25.2 | VTI1A | Intronic | A/T | 0.64/0.58 | 7.30E-03 | 1.19 | 4.32E-08 | 26424050 |
| Melin (2017) | White | GBM | rs11233250 | 11q14.1 | FAM181B | Intergenic | C/T | 0.81/0.87 | 8.72E-04 | 1.24 | 9.95E-10 | 28346443 |
| Melin (2017) | White | Non-GBM | rs7107785 | 11q21 | MAML2 | Intronic | T/C | 0.20/0.48 | 1.01E-40 | 1.16 | 3.87E-10 | 28346443 |
| Kinnersley (2015) | White | Non-GBM | rs648044 | 11q23.2 | ZBTB16 | Intronic | T/C | 0.46/0.39 | 2.46E-03 | 1.25 | 6.26E-11 | 26424050 |
| Shete (2009) | White | Overall | rs498872 | 11q23.3 | PHLDB1 | 5'-UTR | T/C | 0.25/0.31 | 5.80E-03 | 1.18 | 1.07E-08 | 19578367 |
| Chen (2019) | East Asian | Overall | rs498872 | 11q23.3 | PHLDB1 | 5'-UTR | A/G | 0.25/0.31 | 5.80E-03 | 1.25 | 3.41E-09 | 30714141 |
| Chen (2019) | East Asian | Overall | rs10842893 | 12p11.23 | STK38L | Intronic | T/C | 0.03/0.08 | 2.99E-05 | 2.07 | 2.33E-12 | 30714141 |
| Kinnersley (2015) | White | Non-GBM | rs12230172 | 12q21.2 | PHLDA1 | Intergenic | G/A | 0.48/0.54 | 6.52E-03 | 1.23 | 7.53E-11 | 26424050 |
| Kinnersley (2015) | White | GBM | rs3851634 | 12q23.3 | POLR3B | Intronic | T/C | 0.96/0.70 | 1.59E-51 | 1.23 | 3.02E-09 | 26424050 |
| Melin (2017) | White | Non-GBM | rs10131032 | 14q12 | AKAP6 | Intronic | G/A | 0.81/0.92 | 1.56E-11 | 1.33 | 5.07E-11 | 28346443 |
| Chen (2019) | East Asian | Overall | rs4774756 | 15q15-21.1 | RAB27A | Intronic | C/A | 0.30/0.62 | 9.52E-47 | 1.24 | 6.12E-08 | 30714141 |
| Kinnersley (2015) | White | Non-GBM | rs1801591 | 15q24.2 | ETFA | Missense | A/G | 0.06/0.09 | 1.00E-02 | 1.36 | 5.71E-09 | 26424050 |
| Melin (2017) | White | GBM | rs2562152 | 16p13.3 | RHBDF1 | Intergenic | T/A | 0.64/0.85 | 7.30E-28 | 1.21 | 1.93E-08 | 28346443 |
| Melin (2017) | White | Non-GBM | rs3751667 | 16p13.3 | LMF1 | Synonymous | T/C | 0.41/0.21 | 2.78E-23 | 1.18 | 2.61E-09 | 28346443 |
| Melin (2017) | White | GBM | rs10852606 | 16q12.1 | HEATR3 | Intronic | C/T | 0.64/0.71 | 7.95E-04 | 1.18 | 1.29E-11 | 28346443 |
| Stacey (2011) | White | Overall | rs78378222 | 17p13.1 | TP53 | 3'-UTR | C/A | 0.00/0.01 | 0.157 | 2.35 | 1.00E-05 | 21946351 |
| Li (2021) | East Asian | Overall | rs688755 | 19p13.12 | CYP4F12 | Synonymous | C/T | 0.01/0.28 | 8.42E-63 | 3.55 | 2.35E-08 | 34319593 |
| Shete (2009) | White | Overall | rs6010620 | 20q13.33 | RTEL1 | Intronic | G/A | 0.29/0.79 | 4.97E-113 | 1.28 | 2.52E-12 | 19578367 |
| Chen (2019) | East Asian | Overall | rs6010620 | 20q13.33 | RTEL1 | Intronic | G/A | 0.29/0.79 | 4.97E-113 | 1.29 | 7.39E-12 | 30714141 |
| Eckel-Passow (2020) | White | IDH wild-type | rs4809313 | 20q13.33 | GMEB2 | Intronic | G/A | 0.49/0.79 | 1.02E-45 | 1.51/1.59 | 2.60E-10 | 32386320 |
| Melin (2017) | White | GBM | rs2235573 | 22q13.1 | SLC16A8 | Synonymous | G/A | 0.52/0.51 | 6.57E-01 | 1.15 | 1.76E-10 | 28346443 |
aAnnotated by HaploReg website (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php).
bAllele, effect allele/reference allele.
cEAF, effect allele frequency (East Asian/White population) in the 1000 Genomes project.
dChi-square test for the difference in EAF between East Asian and White populations.
eDerived from previous glioma GWASs.
fPubMed ID.
Note: Overall, defined by glioma; GBM, defined by glioblastoma; triple-positive, defined by IDH mutation, TERT mutation and 1p19q co-deletion.