Table 1.

Three independent single nucleotide polymorphisms (SNPs) from high grade glioma discovery GWAS replicated in independent data from the Mayo Clinic. A. Discovery results from the San Francisco Bay Area Adult Glioma Study (AGS) and The Cancer Genome Atlas (TCGA) high grade glioma cases versus AGS and Illumina controls (iControls). B. Replication data from Mayo Clinic high grade glioma cases versus Mayo General Medicine controls. C. Mantel-Haenszel combined p-values.^*

SNP	rs1412829	rs6010620	rs4809324
Chromosome	9	20	20
Position	22033926	61780283	61788664
Gene Symbol		RTEL1	RTEL1
Minor Allele	C	A	C
A. Discovery set: 692 UCSF AGS and TCGA cases and 3992 AGS and iControls
Number genotyped
Cases	692	692	692
Controls	3989	3991	3979
Minor allele frequencies
Cases	0.47	0.17	0.15
Controls	0.39	0.23	0.10
Principal component* adjusted P-value cases versus controls	3.40E-08	1.50E-07	1.50E-07
Odds ratio and 95% confidence intervals for 0, 1, or 2 minor alleles	1.39 (1.24–1.57)	0.68 (0.58–0.79)	1.54 (1.31–1.82)
B. Replication set: 176 Mayo Clinic glioblastoma and anaplastic astrocytoma cases and 174 Mayo Clinic general medicine controls
Number genotyped
Cases	175	175	176
Controls	173	174	174
Minor allele frequencies
Cases	0.53	0.15	0.16
Controls	0.41	0.26	0.10
Principal component* adjusted P-value cases versus controls	0.0038	0.00035	0.03
Odds ratio and 95% confidence intervals for 0, 1, or 2 minor alleles	1.56 (1.16–2.12)	0.48 (0.32–0.72)	1.66 (1.06–2.61)
Combined results
Mantel-Haenszel combined P-values	1.85E-10	3.40E-09	1.70E-09
Odds ratio and 95% confidence intervals	1.42 (1.27–1.58)	0.66 (0.57–0.76)	1.60 (1.37–1.87)

^*Principal component analysis implemented with Eigenstrat software. Complete results for thirteen top hits with p<10⁻⁶ from UCSF GWAS and Mayo Clinic replication p-values are shown in Supplementary Table 2, with Mantel-Haenszel combined results presented in Supplementary Table 6.