Table 1.

Main associations which showed robust evidence from the Mendelian randomisation, colocalisation and Steiger filtering analyses.

Gene	SNP(s)	Tissue	Subtype	OR (95% CI)	P value	H4 (%)	Steiger P value
ABCB6	rs75450661	Brain	All glioma	0.57 (0.44, 0.74)	2.20 × 10–5	97	7.41 × 10–6
BAIAP2L2	rs1004764	Brain	All glioma	0.65 (0.55, 0.78)	1.62 × 10–6	96	2.36 × 10–10
			GBM	0.60 (0.49, 0.73)	2.85 × 10–7	81	1.25 × 10–9
EGFR	rs6979446, rs759170	Brain	GBM	0.45 (0.38, 0.53)	9.99 × 10–20	81	3.53 × 10–6
FAM178B	rs13407036	Brain	All glioma	1.47 (1.23, 1.77)	3.59 × 10–5	94	1.97 × 10–16
JAK1	rs2780902	Brain	All glioma	1.21 (1.13, 1.29)	6.95 × 10–8	81	6.89 × 10–139
			GBM	1.27 (1.17, 1.37)	1.56 × 10–9	95	1.84 × 10–134
MVB12B	rs4837096	Brain	All glioma	1.24 (1.12, 1.38)	5.27 × 10–5	97	2.53 × 10–23
PANK4	rs2985862	Blood	All glioma	0.46 (0.32, 0.67)	4.30 × 10–5	97	4.62 × 10–10
PICK1	rs5756894	Brain	All glioma	1.72 (1.39, 2.14)	8.82 × 10–7	97	4.34 × 10–7
			GBM	1.96 (1.54, 2.51)	6.60 × 10–8	92	2.13 × 10–6
PRLR	rs67975005	Brain	All glioma	0.66 (0.54, 0.82)	9.33 × 10–5	91	1.13 × 10–7
RETREG2	rs1996719	Brain	All glioma	0.68 (0.57, 0.80)	9.54 × 10–6	98	7.90 × 10–11
			GBM	0.67 (0.55, 0.81)	6.13 × 10–5	95	9.91 × 10–11
STMN3	rs6011016	Brain	All glioma	0.36 (0.29, 0.46)	1.44 × 10–16	96	1.44 × 10–16
			GBM	0.29 (0.22, 0.38)	4.55 × 10–19	97	7.88 × 10–3
TP53	rs35850753	Blood	Non-GBM	0.17 (0.09, 0.32)	9.61 × 10–8	98	3.35 × 10–2

The colocalisation result for a single, shared causal variant between the gene and all glioma is provided (“H₄ (%)”, see “Methods” section). Steiger filtering showed the correct orientation for the direction of effect between gene expression and subtype risk for all results in this table.