Table 2.

Prioritized functional SNPs at 1p13.2 locus

SNP ID	MAF	Region	Nearest genes	r 2	P NBa	P CMMb	RE NBc	RE CMMc	RE hNCCc	CADD	FATHMM	GWAVA	DeepSea	TSS
rs61817589	0.22	5′-UTR	PTHF1	0.51	0.112	0.101	32	7	2	19.98	0.94	0.50	0.70	683.3
rs2797412	0.24	Upstream	PTHF1	0.59	0.072	0.213	29	1	2	6.39	0.20	0.52	0.80	457.1
rs2153977	0.28	Intronic	MAGI3	1.00	0.030	0.0003	19	3	2	11.30	0.10	0.35	0.54	171.4
rs4456089	0.22	Intronic	MAGI3	0.72	0.136	0.170	19	4	2	4.92	0.14	0.29	0.51	125.0
rs11102649	0.23	Intronic	MAGI3	0.68	0.162	0.116	24	1	2	4.05	0.15	0.27	0.28	117.4
rs11102648	0.22	Intronic	MAGI3	0.72	0.154	0.102	20	1	2	5.36	0.14	0.20	0.42	104.5
rs10858000	0.22	Intronic	MAGI3	0.72	0.102	0.083	9	1	2	2.91	0.08	0.31	0.36	50.0
rs1775754	0.24	Intronic	PTPN22	0.59	0.058	0.240	4	2	2	1.18	0.03	0.31	0.20	27.6
rs1217421	0.24	Intronic	PTPN22	0.59	0.072	0.205	4	3	2	0.48	0.08	0.23	0.16	26.5

The coefficient r² is calculated with respect to the index SNP: rs2153977. In bold is the index SNP. TSS (tissue-specific score) = 1/(sum of single rank score × 100) × (number of regulatory elements). MAF, minor allele frequency.

^a P-value reported in GWAS data set of NB (stage 1).

^b P-value reported in GWAS data set of CMM (stage 1).

^cRegulatory element (RE): super-enhancer, enhancer or promoter (see Figure 1A; Supplementary Table 10; and Supplementary Material, available at Carcinogenesis Online).