Table 2.

P values for candidate novel risk regions from the discovery, validation, and meta-analysis including the lowest P value SNP from each region

						Region-based analysis				SNP-based meta-analysis				Region-based meta-analysis
						GBJ				Logistic regression				GBJ	MAGMA
						Discovery			Valid’na
						GliomaScan	AGOG	GICC	UCSF/Mayo				Meta-analysis	Meta-analysisa	Meta-analysisa
Locus	Start Mbp	End Mbp	Genes within the region	Glioma type	Sex at risk	P values				No. of SNPs in region	Lowest P value SNP in region	OR	P value	P values
1p36.21	13.9	14.2	PDPN, PRDM2	All glioma	Male	0.025	0.034	0.006	0.470	1,017	rs35042965	0.81	1.54E−06***	0.002**	0.020
2p25.1	11.7	12.1	GREB1, NTSR2, LPIN1	GBM	Female	6.57E−05*	0.001	NA	0.830	1,372	rs72773920	2.15	1.37E−04	0.035	0.077
2q14.3	123.2	123.5	Intergenic	GBM	Male	0.024	0.013	NA	0.085b	979	rs958539	1.50	0.002	0.822	0.907
4q32.3	164.8	165.1	MARCHF1	Non-GBM	Both sexes	0.008	0.035	NA	0.812	1,068	rs114294504	1.79	0.004	0.731	0.254
5q35.2	174.4	174.9	LINC01051, DRD1, SFXN1	All glioma	Male	0.003	0.007	0.555	0.727b	1,806	rs13188939	0.79	5.19E−04	0.348	0.084
7q31.33	125.7	126.5	GRM8	GBM	Male	0.036	5.91E−05*	NA	1.000	2,330	rs11767389	1.29	3.81E−04	0.102	0.127
14q23.2	63.0	63.3	KCNH5	All glioma	Female	0.019	0.005	1.000	0.751	1,009	rs138459733	1.53	0.005	0.293	0.234
14q32.13	96.7	97.0	BDKRB1, ATG2B, GSKIP, AK7	All glioma	Both sexes	0.021	0.256	0.003	0.782	728	rs12050328	0.84	1.62E-04	0.006	0.004**
15q13.3	32.1	32.6	OTUD7A, CHRNA7	All glioma	Male	0.475	0.006	0.014	0.039	878	rs117034591	0.61	0.001	0.006	0.002**
16p13.3	7.0	7.4	RBFOX1	All glioma	Female	0.759	0.018	0.004	0.009	2,789	rs2346609	1.24	3.21E−07***	0.003**	0.001**
16p12.13	20.3	20.7	GP2, UMOD, PDILT, ACSM5, ACSM2A, ACSM2B, ACSM1, THUMPD1, ACSM3	All glioma	Both sexes	0.022	0.002	1.000	1.000c	1,172	rs4643331	1.65	0.004	0.911	0.562

Abbreviations: GBJ, generalized Berk-Jones statistic; Mbp, megabase pair as per hg19 genome build; meta-analysis, GliomaScan, AGOG, GICC, and UCSF/Mayo; Valid’n, validation dataset (UCSF/Mayo).

NA Glioma type information was unavailable for GICC and UCSF/Mayo sex-specific non-GBM summary statistics for 4q32.3 were unavailable.

Bold = P value < 0.05.

*, P value < multiple-testing adjusted threshold in discovery data (P = 0.001 = 0.05/61 regions).

**, P value < multiple-testing adjusted threshold in meta-analysis (P = 0.004 = 0.05/11 regions).

***, P value < multiple-testing adjusted threshold in SNP meta-analysis (P = 3.30E−06 = 0.05/15,148 SNPs).

^aThese analyses were conducted on summary statistics using 1000 genomes as a reference for linkage disequilibrium (LD) estimation.

^b2q14.3 and 5q35.2 regions reported P = 0.011 and P = 0.042 respectively using the combined sex validation data (UCSF/Mayo).

^c16p12.13 region reported P = 0.002 using female validation data (UCSF/Mayo).