Table 2 Known BC susceptibility SNPs demonstrating associations in the BRCA2 case-only analysis.

Location	SNP name^a	Chr^b	Position^c	Nearest gene	Estimated effect allele	Referent allele	Frequency^d	r²	OR^e	P^f	OR_BCAC^g	P_BCAC^h	OR_computedⁱ	Variation in risk^j
5q11.2	rs62355902	5	56053723	MAP3K1	T	A	0.18	0.98	0.89	1.10e⁻⁰⁴	1.18	8.50e⁻⁴²	1.05	TT1
9q31.2	rs10759243	9	110306115	RP11-438P9.2	A	C	0.31	1	0.89	4.60e⁻⁰⁶	1.06	4.20e⁻¹⁰	0.95	TT1
22q13.1	chr22_40876234_C_T	22	40876234	MKL1	C	T	0.11	1	0.88	2.8e⁻⁰⁴	1.12	5.70e⁻¹⁶	0.98	TT1

N = 62,822 breast cancer cases (57,725 BCAC cases and 5,097 BRCA2 mutation carrier cases).
Considering SNPs with known BC (Michailidou et al.)³⁵ associations in the general population.
TT1 tends to 1, ISD increase in same direction, IOD increase in opposite direction.
^aAfter allowing for multiple testing, α* = 2.7 × 10⁻⁴.
^bChromosome.
^cBuild 37 position.
^dFrequency of the allele for which effect is estimated in BCAC cases (OncoArray dataset).
^ePer 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.
^fp-value in the case-only analysis (after allowing for multiple testing, p* = 2.7 × 10⁻⁴).
^gPer allele odds-ratio estimated in BCAC (Michailidou et al.)³⁵.
^hp-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.
ⁱPer allele computed odds-ratio (OR × OR_BCAC).
^jCompared with Michailidou et al’s OR estimates³⁵.

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