Table 3 List of potential novel SNP modifiers associated in the case-only analysis for BRCA1 mutation carriers.

Location	SNP name^a	Chr^b	Position^c	Nearest gene	Localisation	Estimated effect allele	Referent allele	r² ^d	Frequency^e	OR^f	P^g	OR_ER^h	P_ER¯ⁱ	HR_CIMBA^j	P_CIMBA^k	OR_BCAC^l	P_BCAC^m	P_hetⁿ	Target gene^o
11p11.2	rs80221606	11	47560211	CELF1	Intronic	AT	A	0.76	0.10	0.78	1.12e⁻¹⁰	0.76	6.36e⁻⁰⁷	0.98	7.60e⁻⁰¹	1.04	0.01	1.39e⁻⁰³	Level 2
17q21.2	rs58117746	17	39305775	KRTAP4-5	Pepshift	TGGCAGCAGCTGGGGC	T	0.60	0.39	1.18	4.33e⁻¹⁰	1.15	7.71e⁻⁰⁵	1.05	2.20e⁻⁰²	1.02	0.26	4.60e⁻⁰⁴	–
17q21.2	rs5820435	17	39961558	LEPREL4	Intronic	A	C	0.51	0.45	0.82	9.55e⁻¹²	0.85	7.71e⁻⁰⁵	1.01	9.00e⁻⁰¹	1.02	0.07	1.06e⁻⁰⁸	–
17q21.2	rs11079012	17	39912880	JUP	Intronic	G	C	0.66	0.31	1.17	7.06e⁻⁰⁹	1.18	2.35e⁻⁰⁵	0.98	3.10e⁻⁰¹	1.01	0.51	1.15e⁻⁰⁷	Level 2

N = 67,469 breast cancer cases (60,212 BCAC cases and 7,257 BRCA1 mutation carrier cases)
^aThe most significant SNP of each region after allowing for multiple testing, α* = 10⁻⁸
^bChromosome.
^cBuild 37 position.
^dImputation accuracy.
^eFrequency of the allele for which effect is estimated in BCAC cases (OncoArray dataset).
^fPer allele odds ratio estimated in the case-only analysis. OR values were computed from a two sided logistic regression using a 1 df lrtest adjusted for age at BC diagnosis, country and the first four principal components.
^gp-value in the case-only analysis.
^hPer allele odds-ratio estimated in the case-only ER-negative subgroup analysis.
ⁱp-value in the case-only ER-negative subgroup analysis.
^jPer allele hazard ratio estimated in CIMBA cohort analysis.
^kp-value found in CIMBA cohort analysis.
^lPer allele odds-ratio estimated in BCAC (Michailidou et al.)³⁵.
^mp-value in BCAC (Michailidou et al.)³⁵. For SNPs with P_BCAC > 10⁻⁸, significance was attained in merging data of Oncoarray, iCOGS and 11 different breast cancer GWAS in Michailidou et al.³⁵.
ⁿp-value of the heterogeneity test by country.
^oINQUISIT score level: 1 = most functional evidence supporting a potential link between CCVs and target gene.

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