Table 4 List of potential novel SNP modifiers associated in the case-only analysis for BRCA2 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	HR_CIMBA^h	P_CIMBAⁱ	OR_BCAC^j	P_BCAC^k	P_HET^l	Target gene^m
2p14	rs12470785	2	67634003	ETAA1	Intron	G	A	0.98	0.30	0.84	2.83e⁻¹¹	0.89	1.69e⁻⁰⁵	0.98	0.03	2.18e⁻⁰⁷	Level 2
13q13.1	rs79183898	13	32221794	B3GALTL - RXFP2	Intergenic	A	T	0.84	0.07	1.33	2.88e⁻¹⁰	1.04	3.55e⁻⁰¹	1.01	0.54	1.12e⁻⁰⁸	–
13q13.1	rs736596	13	33776506	STARD13	Intron	T	G	0.66	0.09	1.37	3.44e⁻¹²	0.94	2.54e⁻⁰¹	0.98	0.45	4.99e⁻¹¹	Level 1
13q13.2	rs4943263	13	35376357	RP11-266E6.3 - RP11-307O13.1	Intergenic	T	C	0.99	0.27	1.17	8.33e⁻¹¹	1.01	9.83e⁻⁰¹	1.00	0.47	6.94e⁻⁰³	Level 2

N = 62,822 breast cancer cases (57,725 BCAC cases and 5,097 BRCA2 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 hazard ratio estimated in CIMBA cohort analysis.
ⁱp-value found in CIMBA cohort analysis.
^jPer allele odds-ratio estimated in BCAC (Michailidou et al.)³⁵.
^kp-value in BCAC (Michailidou et al. 2017). 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.
^lp-value of the heterogeneity test by country.
^mINQUISIT score level: 1 = most functional evidence supporting potential link between CCVs and target gene.

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