Table 2.

SNP pairs showing evidence for interaction effect on Breslow Thickness

Pathway	SNP	Chromosome	Gene1	Alleles E/R2	EAF2	MELARISK		MDACC		Meta-analysis		Multiple-testing corrected thresholds6
						Interaction effect		Interaction effect		Interaction effect
						βint3 (seint)	pint4	βint3 (seint)	pint4	βmeta-int5 (semeta-int)	pmeta-int5	Tpathway	Toverall
Myeloid cell differentiation
	rs3117048	1p36.1	34kU CDC42	A/G	0.31	0.11	5.6x10−5	0.07	7.1x10−3	0.09	2.2x10−6	7.5x10−6	2.5x10−6
	rs7798406	7p21.3	SCIN (intron)	A/G	0.46	(0.03)		(0.03)		(0.02)
Cytokine activity
	rs9505270	6p24-p23	BMP6 (intron)	A/G	0.27	0.12	2.1x10−5	−0.05	0.05	0.02	0.22	1.5x10−6	5.0x10−7
	rs4276645	8p12	NRG1 (intron)	A/G	0.33	(0.03)		(0.02)		(0.02)
	rs3734034	5q33.3	CYFIP2 (exon)	T/C	0.35	0.10	3.7x10−5	−0.04	0.05	0.02	0.28
	rs2066266	6p22.3	17kD PRL	G/A	0.44	(0.03)		(0.02)		(0.02)

¹Gene symbol; k indicates distance to gene in kilobases (Build 37.1); U indicates "upstream of"; D indicates "downstream of ". Upstream and downstream respectively refer to the 5’ and 3’ ends of the coding strand of each gene.

²E/R=Effect allele/Reference allele; EAF=Effect allele frequency.

³β_int is the regression coefficient of interaction effect between SNPs on Breslow thickness; se_int is the standard error of β_int

⁴p_int is the p-value of the likelihood-ratio test for interaction (one degree of freedom test)

⁵β_meta-int and se_meta-int are the regression coefficient and standard error of interaction effect between SNPs in the meta-analysis of MELARISK and MDACC; p_meta-int is the p-value associated with the Wald test of meta-analysed interaction effect

⁶Tpathway and Toverall are respectively the pathway-corrected and overall-corrected critical thresholds to take into account multiple testing.