Table 1.

Population frequencies of candidate alleles for BC and TNBC-specific risk analyses.

SNP	Associated/neighboring gene	Chr:position	Variant consequence	Minor allele	ICSBCS Cohort*				1000 Genomes**
					AA MAF	EA MAF	G MAF	E MAF	Global MAF	AFR MAF	EUR MAF
rs13000023	TNP1, DIRC3	2:217,924,394	Intron	A	0.219	0.268	0.244	0.155	0.150	0.130	0.210
rs2363956	ANKLE1	19:17,394,124	Missense	G	0.482	0.510	0.490	0.683	0.460	0.500	0.570
rs2981578	FGFR2	10:123,340,311	Intron	T	0.271	0.516	0.364	0.250	0.370	0.080	0.480
rs2981579	FGFR2	10:123,337,335	Intron	G	0.398	0.551	0.449	0.440	0.510	0.340	0.550
rs3112572	CASC16, LOC643714	16:52,600,447	Intron	A	0.216	0.011	0.246	0.207	0.120	0.270	0.030
rs3745185	BABAM1	19:17,384,267	Intron	A	0.191	0.400	0.261	0.369	0.310	0.210	0.480
rs4245739	MDM4	1:204,518,842	3′ UTR	C	0.271	0.321	0.252	0.145	0.210	0.230	0.260
rs4849887	LOC84934, GLI2	2:121,245,122	Intergenic	C	0.349	0.495	0.329	0.440	0.790	0.700	0.900
rs609275	MYEOV, CCND1	11:69,402,915	Regulatory	T	0.491	0.037	0.552	0.085	0.210	0.490	0.000
rs6676002	DARC/ACKR1	1:159,173,144	Upstream	T	0.027	0.212	0.000	0.195	0.090	0.010	0.180
rs3027008	DARC/ACKR1	1:159,173,539	Upstream	T	0.027	0.212	0.012	0.195	0.090	0.010	0.180
rs3027013	DARC/ACKR1	1:159,174,209	5′ UTR	T	0.022	0.087	0.000	0.110	0.030	0.000	0.080
rs71782098	DARC/ACKR1	1:159,174,347	5′ UTR	DEL	0.080	0.021	0.103	0.060	0.030	0.100	0.000
rs2814778	DARC/ACKR1	1:159,174,683	5′ UTR	C	0.797	0.005	0.971	0.533	0.270	0.960	0.010
rs17838198	DARC/ACKR1	1:159,175,005	Intron	T	0.084	0.263	0.005	0.131	0.220	0.010	0.230
rs3027016	DARC/ACKR1	1:159,175,193	Splice/Intron	G	0.045	0.163	0.000	0.037	0.060	0.000	0.160
rs12075	DARC/ACKR1	1:159,175,354	Missense	G	0.128	0.398	0.012	0.207	0.460	0.020	0.400

*African Americans (AA), European Americans (EA), Ghanaians (G), Ethiopians (E).

*MAF = Minor allele frequency.

**1000 Genomes Allele frequencies obtained from ensemble.