Table 1.

Results for top list of SNP–SNP interactions in the CGEMS and JHH populations (P_interaction <1.0E–08 in CGEMS and P_interaction < 0.01 in JHH)

Study	SNP A						SNP B						Interaction	Annotation for SNP A			Annotation for SNP B
	rsID	CHR	BP	A1	MAF	Main effect P	rsID	CHR	BP	A1	MAF	Main effect P	BOOST P	Location	Gene	Relative position	Location	Gene	Relative position
CGEMS	rs7514217	1	13,795,386	G	0.42	0.75	rs7934426	11	37,270,065	G	0.46	0.38	5.3E–09	Intron	PDPN	–	Intergenic	RAG2	−693,660
JHH				G	0.45	0.16				G	0.44	0.37	1.9E–03
CGEMS	rs2503220	1	66,272,145	G	0.08	0.80	rs2579790	10	77,725,730	C	0.38	0.32	9.3E–09	Intron	PDE4B	–	Intron	C10orf11	–
JHH				G	0.08	0.75				C	0.39	0.23	3.1E–03
CGEMS	rs13402702	2	29,033,906	G	0.2	0.05	rs7329899	13	105,276,784	A	0.26	0.99	6.4E–09	Intergenic	SNORD53	30,394	Intergenic	DAOA	335,400
JHH				G	0.18	0.15				A	0.25	0.33	9.0E–03
CGEMS	rs4314028	2	51,990,169	C	0.25	0.41	rs11980379	7	50,437,475	C	0.26	0.49	5.6E-09	Intergenic	CHAC2	−1,858,264	3′UTR	IKZF1	–
JHH				C	0.26	0.99				C	0.26	0.18	3.4E–03
CGEMS	rs4314028	2	51,990,169	C	0.25	0.41	rs4132601	7	50,438,098	G	0.26	0.51	3.4E–09	Intergenic	CHAC2	−1,858,264	3′UTR	IKZF1	–
JHH				C	0.26	0.99				G	0.26	0.14	5.1E–03
CGEMS	rs4664789	2	156,575,782	C	0.49	0.97	rs8019172	14	51,715,669	A	0.1	0.48	8.8E–09	Intergenic	NR4A2	313,408	Intergenic	PTGDR	−88,512
JHH				A	0.49	0.17				A	0.1	0.35	5.8E–03
CGEMS	rs4973194	2	229,945,721	G	0.37	0.49	rs1949403	3	6,070,643	C	0.28	0.26	9.4E–09	Intron	DNER.	–	Intergenic	EDEM1	833,993
JHH				G	0.36	0.91				C	0.27	0.65	8.9E–03
CGEMS	rs6772801	3	140,979,161	G	0.29	0.16	rs6955437	7	137,547,448	T	0.11	0.77	3.9E–09	Intergenic	NMNAT3	−99,631	Intergenic	AKR1D1	93,858
JHH				G	0.27	3.3E–04				T	0.09	0.31	8.9E–03
CGEMS	rs6878100	5	129,370,204	A	0.33	0.77	rs2960753	7	141,386,546	T	0.4	0.47	3.6E–09	Intron	CHSY3	–	Intron	MGAM	–
JHH				A	0.33	0.44				T	0.39	0.39	9.7E–03
CGEMS	rs6948622	7	145,043,041	A	0.36	0.85	rs1154140	14	40,456,756	G	0.3	0.23	8.2E–09	Intergenic	TPK1	−878,962	Intergenic	LRFN5	−689,758
JHH				A	0.34	0.28				G	0.32	0.14	9.2E–03
CGEMS	rs12682543	8	29,135,477	G	0.34	0.04	rs11231168	11	62,158,196	T	0.42	0.23	2.2E–09	Intron	KIF13B	–	Intron	GANAB	–
JHH				G	0.32	0.12				T	0.4	0.34	4.7E–03
CGEMS	rs10810961	9	18,361,966	G	0.10	0.11	rs643853	21	43,656,244	A	0.18	0.05	3.7E–09	Intergenic	MIR3152	−201,338	Intergenic	SIK1	2,583
JHH				G	0.11	0.26				A	0.21	0.22	5.2E–03
CGEMS	rs4837960	9	124,163,792	T	0.15	0.98	rs275769	12	123,687,425	T	0.31	0.45	9.8E–09	Intergenic	PTGS1	−9,258	Intergenic	SCARB1	140,702
JHH				T	0.14	0.45				T	0.3	0.24	8.9E–03
CGEMS	rs1038972	10	31,243,098	T	0.11	0.17	rs2022896	14	27,074,470	A	0.24	0.65	4.2E–09	Intron	ZNF438	–	Intergenic	MIR4307	626,699
JHH				T	0.12	0.33				A	0.25	0.70	7.8E–03
CGEMS	rs12861843	13	35,638,422	C	0.42	0.06	rs3862743	13	41,208,633	C	0.39	0.34	4.1E-09	Intergenic	SOHLH2	1,923	Intron	KIAA0564.	–
JHH				C	0.45	0.91				C	0.4	0.28	3.2E–03
CGEMS	rs2136267	13	107,332,783	T	0.25	0.37	rs1884393	20	1,404,079	A	0.11	0.46	9.3E–09	Intergenic	LIG4	325,010	3′UTR	SIRPB2	–
JHH				T	0.27	0.33				A	0.11	0.95	6.5E–03

Main effect P refers to the single-locus P value based on the two-degree of freedom test; BOOST P refers to the P values for the multiplicative interaction term, as calculated by BOOST approach. Relative position is the distance of SNPA/SNPB relative to the nearest gene if SNPA/SNPB is located in the intergenic region

SNP A the first interacting SNP, SNP B the second interacting SNP, CHR chromosome, MAF minor allele frequency, CGEMS the Cancer Genetic Markers of Susceptibility, JHH Johns Hopkins Hospital