Table 2.

Risk loci for breast cancer identified in the EUGENE gene-based analysis but not in previous GWAS

Locus index	Gene	Chr	Start	N sentinel eQTL		Gene-based P-valuea	Sentinel eQTL with strongest association in the adjusted GWAS		OncoScore
				Tested	with P < 0.05 in adjusted GWASb		Variant	P-valueb
1	GSTM2	1	110210644	14	5	6.63E−08	rs621414	4.08E−05	38.97
2	SEMA4A	1	156117157	9	5	1.45E−07	rs887953	2.39E−06	27.04
3	LINC00886	3	156465135	1	1	2.34E−06	rs7641929	2.34E−06	N/A
4	AC034220.3	5	131646978	7	4	5.92E−07	rs11739622	0.000314	N/A
4	IRF1	5	131817301	2	2	4.99E−07	rs2548998	3.44E−05	42.46
5	SIK2	11	111473115	2	2	4.09E−07	rs527078	3.32E−05	39.57
5	PPP2R1B	11	111597632	8	2	2.31E−06	rs680096	2.91E−06	56.52
6	MAN2C1	15	75648133	14	6	1.91E−06	rs8028277	2.16E−06	26.66
6	RP11-817O13.8	15	75660496	4	4	3.83E−08	rs4545784	3.85E−06	N/A
6	SIN3A	15	75661720	4	4	3.83E−08	rs4545784	3.85E−06	42.43
6	IMP3	15	75931426	1	1	2.30E−06	rs4886708	2.30E−06	80.41

^aGene-based association P-value obtained when the EUGENE gene-based test was applied to the adjusted GWAS results

^bP-value in the Michailidou et al. ². GWAS, adjusted for (i) the association with the sentinel risk variants identified in this study using the COJO-COND test; and (ii) the LD-score intercept