Table 2 Genes associated with breast cancer risk at the Bonferroni-corrected significant level of 0.05

Breast cancer subtype^a	Gene	Cytoband	Nearest index SNP^b	Z score	P value
Exp-TWAS
Overall	CTD-3080P12.3	5p15.33	rs2853669	4.7	3.2 × 10⁻⁶
ER-Neg^d	EN1	2q14.2	rs76664032^c	−5.7	1.6 × 10⁻⁸
ER-Neg^d	LINC01956	2q14.2	rs76664032^c	−5.4	5.3 × 10⁻⁸
TNBC^d	EN1	2q14.2	rs76664032^c	−5.8	6.9 × 10⁻⁹
TNBC^d	LINC01956	2q14.2	rs76664032^c	−5.6	2.5 × 10⁻⁸
APA-WAS
Overall	TET2	4q24	rs62331150	−4.4	1.2 × 10⁻⁵
ER-Neg	TET2	4q24	rs62331150	−4.9	1.2 × 10⁻⁶
spTWAS
Overall	BRD9	5p15.33	rs2853669	−4.7	2.3 × 10⁻⁶
Overall	NUP210L	1q21.3	/	−4.7	3.0 × 10⁻⁶
ER-Neg	BRD9	5p15.33	rs2853669	−5.2	2.2 × 10⁻⁷
TNBC	BRD9	5p15.33	rs2853669	−4.8	1.8 × 10⁻⁶

P values were derived from the Z score tests (two-sided). Statistical significant threshold for multiple comparison adjustment is defined as P < 5.0 × 10⁻⁶ for gene expression TWAS of 9982 tests (0.05/9982), P < 1.5 × 10⁻⁵ for APA-WAS of 3309 tests (0.05/3309), and P < 4.3 × 10⁻⁶ for spTWAS of 11,426 tests (0.05/11,426) using Bonferroni correction.
^aER-Pos estrogen receptor (ER)-positive, ER-Neg ER-negative, TNBC triple-negative breast cancer, TWAS transcriptome-wide association study, Exp-TWAS gene expression TWAS, APA-WAS alternative polyadenylation (APA)-wide association study, spTWAS splicing TWAS.
^bWithin ± 500 Kb region.
^cThis index SNP (rs76664032) was identified in our recent GWAS conducted among AA female participants.
^dSuggestive associations were found for genes CTD-3080P12.3 (P = 1.3 × 10⁻⁵) with ER-negative breast cancer risk and MRPL34 (P = 9.2 × 10⁻⁶) with TNBC risk at the p value near the significant threshold after Bonferroni correction.

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