Table 1 Genome-wide significant loci for mammographic density phenotypes identified in the meta-analysis of Hologic and GE studies.

From: Identification of 31 loci for mammographic density phenotypes and their associations with breast cancer risk

Region^a	Lead SNP	Position	Gene^b	Ref/Alt	AAF	Hologic (N = 20,311)			GE (N = 3881)			Combined (N = 24,192)
Region^a	Lead SNP	Position	Gene^b	Ref/Alt	AAF	Beta	SE	P value	Beta	SE	P value	Beta	SE	P value
Dense area (n = 16)
1p32.3	rs6703250	51418472	FAF1	C/T	0.55	−0.052	0.009	9.8E–08	−0.068	0.022	2.0E–03	−0.054	0.009	4.8E–10
2p24.1	rs11684853	19310918	OSR1	G/T	0.55	0.049	0.009	2.0E–07	0.047	0.022	3.1E–02	0.049	0.009	2.5E–08
2p13.1	rs6715731	74346404	TET3, BOLA3	G/T	0.42	−0.055	0.009	7.7E–09	−0.006	0.022	8.0E–01	−0.048	0.009	4.7E–08
2q35	rs66470855*	218266438	TNS1	TG/T	0.26	0.061	0.011	1.3E–08	0.058	0.025	2.0E–02	0.060	0.010	8.5E–10
3p25.2	rs67901221	12416550	PPARG	A/G	0.15	0.079	0.013	1.5E–09	0.012	0.030	6.8E–01	0.069	0.012	1.4E–08
4q28.1	rs1503613	127772368	—	G/T	0.47	0.059	0.009	4.5E–10	0.029	0.022	1.9E–01	0.054	0.009	6.1E–10
5q23.2(2)	rs6885843	126068500	TEX43, LMNB1	C/T	0.40	0.051	0.009	1.2E–07	0.032	0.022	1.5E–01	0.048	0.009	4.3E–08
6p22.3	rs3819405*	16399557	ATXN1	C/T	0.33	−0.069	0.010	3.7E–12	−0.067	0.023	3.8E–03	−0.069	0.009	4.4E–14
10p12.1	rs2642278	27936562	RAB18, MKX	T/C	0.36	0.052	0.009	6.5E–08	0.037	0.023	1.0E–01	0.050	0.009	1.0E–08
10q21.1	rs1892368	53674795	PRKG1	G/A	0.67	−0.043	0.010	1.3E–05	−0.090	0.023	9.0E–05	−0.051	0.009	2.4E–08
11p15.4	rs11040963	6713214	MRPL17, OR2AG2	C/A	0.28	−0.052	0.010	7.8E–07	−0.059	0.024	1.5E–02	−0.053	0.010	2.1E–08
12p12.1	rs1818476	26445564	SSPN, ITPR2	C/T	0.75	−0.049	0.011	7.2E–06	−0.089	0.025	4.0E–04	−0.055	0.010	2.4E–08
14q24.1	rs75197674	68971452	RAD51B	T/C	0.21	−0.064	0.012	1.2E–07	−0.065	0.028	2.1E–02	−0.064	0.011	5.9E–09
18q21.33	rs11877925	60896694	BCL2	G/A	0.22	−0.053	0.011	2.6E–06	−0.093	0.026	3.4E–04	−0.060	0.010	7.4E–09
19q13.33	rs492602	49206417	FUT2	A/G	0.48	−0.055	0.009	4.7E–09	−0.084	0.022	1.5E–04	−0.060	0.009	6.9E–12
20q13.13	rs17196752	48887268	SMIM25	C/T	0.20	0.066	0.012	5.1E–08	0.050	0.028	7.0E–02	0.063	0.011	9.2E–09
Non-dense area (n = 13)
1p36.11	rs61777307	23959319	MDS2	G/A	0.24	−0.040	0.008	2.8E–07	−0.055	0.018	2.1E–03	−0.042	0.007	3.5E–09
1p12(1)	rs10802015	118782659	SPAG17	C/T	0.34	−0.039	0.007	3.0E–08	−0.052	0.017	2.0E–03	−0.041	0.007	2.1E–10
1p12(2)	rs1779445	119508412	TBX15	T/C	0.80	0.056	0.008	1.1E–11	0.032	0.019	9.1E–02	0.052	0.008	6.2E–12
2p23.3	rs6718628	25131170	ADCY3	C/G	0.40	0.038	0.007	3.9E–08	0.056	0.016	6.5E–04	0.041	0.006	1.1E–10
2q14.2(2)	rs11123556	121245996	INHBB, GLI2	A/G	0.89	−0.071	0.011	2.2E–11	−0.098	0.025	7.1E–05	−0.075	0.010	9.2E–15
3p25.2	rs199689761	12441088	PPARG	T/TA	0.16	−0.048	0.009	1.2E–07	−0.037	0.021	7.9E–02	−0.047	0.008	2.4E–08
3p14.1	rs4132228	64708114	ADAMTS9	C/T	0.31	−0.045	0.007	2.8E–10	−0.062	0.016	1.5E–04	−0.048	0.007	2.3E–13
6p25.1	rs1294419	6742549	LY86, RREB1	C/G	0.62	0.039	0.007	8.0E–09	0.031	0.016	5.0E–02	0.038	0.006	8.3E–10
10q21.2(1)	rs1949355	64218423	ZNF365	G/A	0.56	−0.039	0.007	3.6E–09	−0.037	0.015	1.7E–02	−0.039	0.006	1.7E–10
11p15.2	rs60521023	13314102	ARNTL	A/AT	0.70	0.041	0.007	2.1E–08	0.042	0.017	1.3E–02	0.041	0.007	7.5E–10
11q24.3	rs2875238	130282078	ADAMTS8	T/C	0.66	0.046	0.007	1.0E–10	0.016	0.017	3.3E–01	0.041	0.007	2.5E–10
12q22	rs11836367	96027467	USP44, NTN4	C/T	0.33	0.045	0.008	2.0E–08	0.030	0.018	1.0E–01	0.042	0.007	8.4E–09
15q25.2	rs1812707	84547222	ADAMTSL3	C/T	0.50	0.032	0.007	1.8E–06	0.044	0.016	5.0E–03	0.034	0.006	3.1E–08
Percent density (n = 12)
2p24.1	rs34331777	19441251	OSR1	CA/C	0.60	0.041	0.008	2.5E–07	0.052	0.019	5.4E–03	0.042	0.007	4.5E–09
2p23.3	rs11676272	25141538	ADCY3	A/G	0.47	−0.040	0.008	2.9E–07	−0.061	0.019	1.1E–03	−0.043	0.007	2.2E–09
2q35	rs66470855*	218266438	TNS1	TG/T	0.26	0.046	0.009	1.8E–07	0.043	0.021	4.1E–02	0.046	0.008	2.0E–08
3p25.2	rs76643909	12441367	PPARG	T/G	0.16	0.076	0.011	1.5E–12	0.029	0.025	2.6E–01	0.069	0.010	4.9E–12
4q28.1	rs35589286	128192680	INTU	G/C	0.29	0.045	0.009	2.1E–07	0.045	0.021	3.0E–02	0.045	0.008	2.0E–08
6p22.3	rs3819405*	16399557	ATXN1	C/T	0.33	−0.058	0.008	1.1E–12	−0.061	0.019	1.9E–03	−0.059	0.008	5.0E–15
8p12	rs6558136	29523123	DUSP4, SARAF	C/T	0.65	−0.038	0.008	3.8E–06	−0.070	0.019	3.2E–04	−0.042	0.008	1.4E–08
10q21.2(1)	rs2138555	64220494	ZNF365	A/G	0.41	−0.054	0.008	4.8E–12	−0.073	0.018	7.8E–05	−0.057	0.007	2.3E–15
11q24.3	rs6590455	130276427	ADAMTS8	T/C	0.65	−0.046	0.008	1.6E–08	−0.012	0.019	5.3E–01	−0.041	0.008	5.0E–08
13q13.3	rs10219975	36269125	NBEA, DCLK1	G/C	0.32	−0.047	0.009	5.8E–08	−0.032	0.020	1.1E–01	−0.045	0.008	1.4E–08
15q26.1	rs4777948	94298239	—	G/T	0.47	0.048	0.008	1.4E–09	0.032	0.019	8.4E–02	0.046	0.007	2.8E–10
19q13.33	rs1704773	49209566	FUT2, MAMSTR	A/G	0.49	−0.040	0.008	4.6E–07	−0.062	0.019	1.2E–03	−0.044	0.007	3.5E–09

^aIndependent regions within the same cytoband are denoted by (1) or (2) in order by position.
^bNearest flanking protein coding gene(s) within 500 kb of the lead SNP.
*Denotes lead SNPs associated with both DA and PD at the genome-wide significance level of p < 5 × 10⁻⁸.

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Table 1 Genome-wide significant loci for mammographic density phenotypes identified in the meta-analysis of Hologic and GE studies.

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