Genome-wide and transcriptome-wide association studies of mammographic density phenotypes reveal novel loci

Chen, Hongjie; Fan, Shaoqi; Stone, Jennifer; Thompson, Deborah J.; Douglas, Julie; Li, Shuai; Scott, Christopher; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Michailidou, Kyriaki; Li, Christopher; Peters, Ulrike; Hopper, John L.; Southey, Melissa C.; Nguyen-Dumont, Tu; Nguyen, Tuong L.; Fasching, Peter A.; Behrens, Annika; Cadby, Gemma; Murphy, Rachel A.; Aronson, Kristan; Howell, Anthony; Astley, Susan; Couch, Fergus; Olson, Janet; Milne, Roger L.; Giles, Graham G.; Haiman, Christopher A.; Maskarinec, Gertraud; Winham, Stacey; John, Esther M.; Kurian, Allison; Eliassen, Heather; Andrulis, Irene; Evans, D. Gareth; Newman, William G.; Hall, Per; Czene, Kamila; Swerdlow, Anthony; Jones, Michael; Pollan, Marina; Fernandez-Navarro, Pablo; McConnell, Daniel S.; Kristensen, Vessela N.; Rothstein, Joseph H.; Wang, Pei; Habel, Laurel A.; Sieh, Weiva; Dunning, Alison M.; Pharoah, Paul D. P.; Easton, Douglas F.; Gierach, Gretchen L.; Tamimi, Rulla M.; Vachon, Celine M.; Lindström, Sara

doi:10.1186/s13058-022-01524-0

Breast Cancer Research

Table 2 Association between MD significant loci and breast cancer risk (overall, ER-positive, and ER-negative)

From: Genome-wide and transcriptome-wide association studies of mammographic density phenotypes reveal novel loci

Region	rsID	CHR	Position¹	Allele²	MD phenotype		Overall breast cancer⁴			ER-positive breast cancer⁴			ER-negative breast cancer⁴
Region	rsID	CHR	Position¹	Allele²	Z-score	p Value	Beta	SE³	p Value	Beta	SE	p Value	Beta	SE	p Value
DA
1q21.2	rs11205303	1	149,906,413	T/C	− 6.772	1.25 E−11	0.050	0.006	1.05 E−14	0.057	0.008	8.25 E−14	0.040	0.012	6.67 E−04
2q14.2	rs17625845	2	121,089,731	T/C	7.949	1.87 E−15	− 0.046	0.008	1.73 E−08	− 0.032	0.010	8.94 E−04	− 0.114	0.015	1.13 E−13
4q13.3	rs6851733	4	75,518,708	T/C	6.874	6.23 E−12	0.009	0.008	2.20 E−01	0.001	0.009	9.58 E−01	0.018	0.014	1.97 E−01
5q11.2	rs150249911	5	52,119,132	A/G	− 5.928	3.06 E−09	0.038	0.027	1.49 E−01	0.048	0.032	1.33 E−01	0.053	0.050	2.87 E−01
5q23.2	rs335189	5	122,446,856	C/G	6.655	2.84 E−11	0.027	0.007	8.38 E−05	0.026	0.008	1.46 E−03	0.012	0.012	3.32 E−01
5q35.1	rs2042239	5	169,566,329	A/G	6.485	8.87 E−09	0.028	0.006	9.80 E−06	0.037	0.008	1.02 E−06	0.003	0.012	7.72 E−01
6q25.1	rs9397436	6	151,952,002	A/G	7.951	1.86 E−15	0.184	0.012	2.00 E−54	0.138	0.014	1.71 E−22	0.272	0.021	4.01 E−40
7p11.2	rs10155920	7	55,308,930	T/C	5.755	8.66 E−09	0.011	0.008	2.01 E−01	0.012	0.010	2.50 E−01	− 0.001	0.015	9.35 E−01
8q24.13	rs58847541	8	124,610,166	A/G	5.994	2.05 E−09	− 0.063	0.009	4.33 E−13	− 0.055	0.010	1.17 E−07	− 0.077	0.016	1.00 E−06
10q21.2	rs10995187	10	64,273,026	A/G	8.933	4.14 E−19	0.129	0.009	2.85 E−49	0.134	0.011	1.74 E−37	0.092	0.016	8.18 E−09
11p15.5	rs4980383	11	1,902,097	T/C	− 7.228	4.90 E−13	− 0.076	0.006	4.36 E−34	− 0.083	0.007	6.20 E−29	− 0.051	0.011	8.31 E−06
12p12.1	rs11836164	12	26,446,625	T/C	6.028	1.66 E−09	− 0.013	0.007	6.81 E−02	− 0.003	0.009	7.32 E−01	− 0.025	0.013	5.78 E−02
12p11.2	rs7297051	12	28,174,817	T/C	6.166	7.01 E−10	0.120	0.007	1.73 E−60	0.110	0.009	3.49 E−36	0.140	0.014	6.45 E−25
12q23.2	rs833472	12	103,005,100	T/C	7.134	9.76 E−13	0.078	0.020	7.59 E−05	0.085	0.024	3.04 E−04	0.049	0.037	1.80 E−01
19q13.33	rs1231281	19	49,239,200	A/G	6.860	6.87 E−12	− 0.008	0.006	2.30 E−01	− 0.010	0.008	2.07 E−01	− 0.002	0.012	8.72 E−01
20q13.13	rs17789629	20	48,892,374	A/C	− 5.478	4.30 E−08	− 0.011	0.008	1.32 E−01	− 0.001	0.009	9.48 E−01	− 0.034	0.014	1.44 E−02
22q13.1	rs34066050	22	38,612,604	A/G	− 5.534	3.14 E−08	− 0.034	0.006	5.58 E−08	− 0.042	0.008	2.35 E−08	− 0.010	0.011	3.78 E−01
22q13.2	rs6001939	22	40,892,794	T/C	8.791	1.48 E−18	− 0.117	0.010	1.31 E−32	− 0.106	0.012	1.20 E−19	− 0.115	0.018	8.77 E−11
NDA
1p12	rs78395856	1	119,495,096	A/C	5.525	3.29 E−08	− 0.037	0.018	3.46 E−02	− 0.044	0.021	3.31 E−02	− 0.037	0.031	2.35 E−01
5q14.1	rs413472	5	80,930,992	T/C	5.551	2.84 E−08	0.004	0.006	5.49 E−01	0.010	0.008	2.11 E−01	− 0.012	0.012	3.18 E−01
8p11.23	rs16885613	8	36,848,357	T/C	− 12.788	1.92 E−37	− 0.076	0.008	1.58 E−20	− 0.070	0.010	5.06 E−13	− 0.099	0.015	2.38 E−11
10q21.2	rs2138555	10	64,220,494	A/G	5.900	3.63 E−09	− 0.044	0.006	1.48 E−12	− 0.047	0.008	3.89 E−10	− 0.030	0.011	8.58 E−03
12q22	rs61938093	12	96,026,737	T/C	− 6.266	3.72 E−10	0.089	0.007	1.34 E−38	0.091	0.008	5.53 E−28	0.069	0.013	3.39 E−08
22q13.2	rs73169097	22	41,027,870	T/C	6.012	1.83 E−09	− 0.120	0.010	1.98 E−34	− 0.110	0.012	5.34 E−21	− 0.117	0.018	4.33 E−11
PMD
1q21.2	rs1868992	1	149,908,108	A/G	5.517	3.44 E−08	− 0.027	0.007	1.64 E−04	− 0.029	0.008	7.09 E−04	− 0.030	0.013	1.98 E−02
5q23.2	rs335189	5	122,446,856	C/G	6.196	5.78 E−10	0.027	0.007	8.38 E−05	0.026	0.008	1.46 E−03	0.012	0.012	3.32 E−01
5q31.1	rs76876329	5	131,237,759	T/C	5.530	3.21 E−08	0.012	0.009	1.87 E−01	0.007	0.011	5.11 E−01	0.014	0.017	3.99 E−01
5q33.3	rs11745230	5	158,171,008	T/G	− 5.793	6.90 E−09	− 0.064	0.008	1.30 E−14	− 0.065	0.010	3.47 E−11	− 0.068	0.015	6.72 E−06
5q35.1	rs2112670	5	169,557,594	A/G	− 5.598	2.17 E−08	− 0.013	0.006	4.71 E−02	− 0.023	0.008	2.83 E−03	0.012	0.012	3.03 E−01
6p22.3	rs3819405	6	16,399,557	T/C	5.806	6.42 E−09	0.040	0.007	1.25 E−08	0.045	0.008	5.38 E−08	0.027	0.013	3.45 E−02
6q25.1	rs4897107	6	149,601,591	T/C	6.842	7.81 E−12	0.036	0.008	5.98 E−06	0.049	0.010	3.55 E−07	0.018	0.015	2.15 E−01
6q25.1	rs9397436	6	151,952,002	A/G	7.303	2.81 E−13	0.184	0.012	2.00 E−54	0.138	0.014	1.71 E−22	0.272	0.021	4.01 E−40
8p11.23	rs10087804	8	36,858,140	C/G	6.282	3.35 E−10	− 0.077	0.008	8.34 E−21	− 0.071	0.010	3.64 E−13	− 0.098	0.015	6.55 E−11
10q21.2	rs10995187	10	64,273,026	A/G	10.424	1.92 E−25	0.129	0.009	2.85 E−49	0.134	0.011	1.74 E−37	0.092	0.016	8.18 E−09
11p15.5	rs4980383	11	1,902,097	T/C	− 5.860	4.62 E−09	− 0.076	0.006	4.36 E−34	− 0.083	0.007	6.20 E−29	− 0.051	0.011	8.31 E−06
12q23.2	rs61941038	12	102,989,316	A/T	− 6.477	9.37 E−11	− 0.075	0.020	1.47 E−04	− 0.085	0.024	3.07 E−04	− 0.032	0.037	3.86 E−01
15q26.1	rs4499190	15	94,275,057	G/C	− 5.654	1.57 E−08	− 0.001	0.007	8.90 E−01	0.001	0.009	8.71 E−01	− 0.008	0.013	5.69 E−01
16q12.2	rs11646715	16	53,824,007	A/G	7.183	6.84 E−13	0.046	0.006	6.89 E−13	0.042	0.008	4.14 E−08	0.055	0.012	1.60 E−06
19q13.33	rs12462111	19	49,171,306	T/C	5.847	5.02 E−09	− 0.017	0.007	1.03 E−02	− 0.015	0.008	5.32 E−02	− 0.011	0.012	3.51 E−01

¹Genomic positions based on build GRCh37/hg19
²Coded as reference allele/effect allele
³Standard error
⁴Beta estimates, SEs, and p values of overall, ER-positive, and ER-negative breast cancer were based on the GWAS results published by the Breast Cancer Association Consortium (BCAC)

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