Table 3. Top 20 SNPs for inherited variant effects on young-onset breast cancer in non-Hispanic white women in the Sister Study and Two Sister Study (n=1279 cases).

Rank	SNP	Allelea	Chromosome	Positionb	Locus	MAFc	RR (95% CI)	P-value	FDR
1	rs28373882	C/T	4	68167336	4q	0.14	1.68 (1.36, 2.05)	2.8 × 10−7	0.17
2	rs879162	C/T	16	26501018	16p	0.22	1.50 (1.27, 1.76)	9.1 × 10−7	0.18
3	rs12606061	T/C	18	30843416	CCDC178	0.15	0.63 (0.52, 0.76)	9.1 × 10−7	0.18
4	rs4784227	T/C	16	52599188	TOX3	0.28	1.45 (1.24, 1.69)	2.1 × 10−6	0.32
5	rs8064617	G/A	17	49742142	CA10	0.32	1.43 (1.23, 1.66)	2.7 × 10−6	0.32
6	rs169409	T/C	20	56240827	PMEPA1	0.41	1.38 (1.20, 1.59)	3.7 × 10−6	0.37
7	rs7952757	C/T	12	114085798	12q	0.32	1.40 (1.21, 1.62)	5.7 × 10−6	0.49
8	rs4784220	C/T	16	52535810	TOX3	0.40	1.37 (1.19, 1.58)	7.7 × 10−6	0.57
9	rs2727565	A/C	7	151321161	PRKAG2	0.27	0.70 (0.60, 0.82)	9.0 × 10−6	0.57
10	rs11042856	A/G	11	10519316	AMPD3	0.34	1.39 (1.20, 1.62)	1.0 × 10−5	0.57
11	rs6572349	T/C	14	22736248	14q	0.12	0.63 (0.52, 0.78)	1.1 × 10−5	0.57
12	rs7155927	G/A	14	22730981	14q	0.13	0.64 (0.52, 0.78)	1.3 × 10−5	0.57
13	rs10409518	T/C	19	16606070	CALR3	0.12	1.63 (1.30, 2.05)	1.3 × 10−5	0.57
14	rs17015190	G/A	4	90138063	4q	0.14	0.66 (0.55, 0.80)	1.4 × 10−5	0.57
15	rs3803662	A/G	16	52586341	TOX3	0.30	1.39 (1.20, 1.61)	1.4 × 10−5	0.57
16	rs16971851	A/G	15	33812509	RYR3	0.23	1.41 (1.20, 1.66)	2.1 × 10−5	0.73
17	rs13430186	G/T	2	170887864	UBR3	0.26	1.41 (1.20, 1.65)	2.2 × 10−5	0.73
18	rs875622	A/G	19	16467759	EPS15L1	0.21	1.45 (1.22, 1.72)	2.2 × 10−5	0.73
19	rs10792551	C/A	11	70927063	SHANK2	0.42	0.75 (0.65, 0.86)	2.4 × 10−5	0.77
20	rs9878305	G/A	3	29335426	RBMS3	0.12	0.66 (0.54, 0.80)	3.0 × 10−5	0.77

^aMinor/major allele coding; the minor allele is the index allele.

^bBased on genomic reference sequence hg19.

^cMinor allele frequency in parents.