Table 5.

List of most significant SNPs in the CCV analysis for BRCA1 mutation carriers.

Fine mapping regiona	Signalb	#CCVc	Location	SNP named	Chre	Positionf	Nearest gene	Localisation	Estimated effect allele	Referent Allele	Frequency g	r² h	Pi	ORj	PERk	ORl	PCIMBAm	HRCIMBAn
chr11:46773616-47773616	1	74	11p11.2	rs60882887	11	47475675	RAPSN, CELF1	Intergenic	A	G	0.14	0.95	2.20e−10	0.82	3.20e−06	0.82	7.00e−01	0.99
chr17:39141815-40141815	1	2	17q21.2	rs5820435	17	39961558	LEPREL4	Intronic	A	C	0.45	0.51	1.10e−11	0.82	2.80e−05	0.85	9.10e−01	1.00
	2	2	17q21.2	rs7222250	17	39938469	JUP	Intronic	C	T	0.44	0.66	5.50e−14	1.23	3.90e−07	1.20	8.70e−01	1.00
	3	6	17q21.2	rs9901834	17	39926811	JUP	Intronic	A	G	0.10	0.55	7.20e−10	0.72	3.90e−06	0.72	7.40e−01	1.02
	4	3	17q21.2	rs58117746	17	39305775	KRTAP4-5	Intronic	TGGCAGCAGCTGGGGC	T	0.39	0.60	5.50e−09	1.17	4.60e−04	1.13	2.20e−02	1.06
	5	13	17q21.2	rs2239711	17	39633317	KRT35	Intronic	A	G	0.29	0.93	4.90e−11	0.85	2.90e−04	0.88	5.00e−01	0.98
	6	4	17q21.2	rs10708222	17	40137437	DNAJC7	Intronic	T	TA	0.17	0.60	8.40e−07	1.18	6.10e−04	1.17	2.28e−01	0.95
	7	4	17q21.2	rs41283425	17	39925713	JUP	Intronic	T	C	0.06	0.54	4.30e−07	0.73	1.30e−05	0.69	4.82e−01	0.95
	8	15	17q21.2	rs56291217	17	39858199	JUP	Intronic	AT	A	0.44	0.76	6.70e−08	0.88	1.20e−06	0.85	4.06e−01	1.03
	9	1	17q21.2	rs111637825	17	40134782	DNAJC7	Intronic	A	G	0.06	0.89	3.60e−07	0.74	3.50e−04	0.75	4.47e−01	0.96

N = 67,469 breast cancer cases (60,212 BCAC cases and 7,257 BRCA1 mutation carrier cases).

^aSignificant region in the main analysis used to look for credible causal variants (CCV).

^bSignal number (the first one corresponds to the CCV set without any adjustment and the following are those with adjustment on each most significant SNP of the previous signals).

^cNumber of credible causal variants at each signal (SNP with p-value at 2 order of magnitude of the most significant one).

^dThe most significant SNP after adjustment on the most significant SNPs of the previous signals (except for these of the signal 1).

^eChromosome.

^fBuild 37 position.

^gFrequency of the allele for which effect is estimated in BCAC cases (OncoArray dataset).

^hImputation accuracy.

ⁱp-value in the case-only analysis after adjustment on the most significant SNPs of the previous signals (except for these of the signal 1).

^jPer allele odds ratio estimated in the case-only analysis. OR values were computed from a two sided logistic regression using a 1df lrtest adjusted for age at BC diagnosis, country, the first four principal components and the most significant SNPs of the previous signals (except for these of the signal 1).

^kP-value in the case-only analysis restricted to ER-negative BCAC cases and after adjustment with the most significant SNP of the previous signals (except for these of the signal 1).

^lPer allele odds ratio estimated in the case-only analysis restricted to ER-negative BCAC cases and after adjustment with the most significant SNP of the previous signals (except for these of the signal 1).

^mp-value found in CIMBA cohort analysis.

ⁿ Per allele hazard ratio estimated in CIMBA cohort analysis.