Table 3.

Novel pleiotropic associations with cutaneous melanoma and nevus count or hair color. Reported cutaneous melanoma P-values are from the total fixed-effects inverse-variance weighted meta-analysis of logistic regression two-sided P-values from GWAS representing a total of 36,760 melanoma cases and 375,188 controls (Online Methods). Results for the lead variants from pleiotropic loci (lead SNP reaching P < 5 × 10⁻⁸ following a Stouffers sample size weighted meta-analysis of cutaneous melanoma P-values and either Nevus GWAS meta-analysis (N = 65,777) or Hair Color GWAS (N=352,662) and GWAS-PW Model 3 prior probability of association (PPA) > 0.5, Online Methods) distinct to those in the total cutaneous melanoma meta-analysis (Table 1, 2). CHR, BP: hg19 positional information. rsID: dbSNP142 rs number. Gene prioritizes genes that the variant is an eQTL for in GTEx skin datasets or otherwise is the closest protein coding gene; multiple indicates three or more genes. We report the total cutaneous melanoma meta-analysis P (CM P), and the CM+nevus or CM+hair color Stouffer’s meta-analysis fixed effect P-value. Full results can be found in Supplementary Tables 7 and 10.

CHR:BP	rsID	Gene	CM P	CM + Nevus P	CM + Hair P
1:24787947	rs195720	NIPAL3	7.97 × 10−6	-	2.24 × 10−12
1:78450517	rs34517439	DNAJB4	2.23 × 10−4	-	2.17 × 10−12
1:214673271	rs7533482	PTPN14	2.79 × 10−5	-	2.45 × 10−13
2:135430709	rs6745983	TMEM163	1.69 × 10−3	-	7.00 × 10−13
2:214065880	rs16849932	IKZF2	1.46 × 10−3	-	1.18 × 10−10
2:240065356	rs11677464a	HDAC4	4.00 × 10−5	1.10 × 10−9	-
4:37470753	rs11730662	KIAA1239	1.82 × 10−3	1.19 × 10−8	-
5:56011357	rs7714232	MAP3K1	6.99 × 10−4	-	3.32 × 10−22
6:7189567	rs75818295	RREB1	1.87 × 10−3	-	8.27 × 10−10
6:11637483	rs548304	ADTRP	2.67 × 10−5	-	1.46 × 10−10
6:15503696	rs10949304	DTNBP1	1.7 × 10−3	4.96 × 10−9	-
6:50790642	rs2857482	TFAP2B	3.59 × 10−5	3.44 × 10−10	-
6:151577739, 6:151577830	rs10434895, rs10434896b	AKAP12	8.17 × 10−8, 7.88 × 10−8	7.71 × 10−10	2.07 × 10−42
8:131138979	rs111595456	ASAP1	3.86 × 10−4	2.83 × 10−10	-
9:211762, 9:235201	rs520015, rs593179a,c	CBWD1	8.95 × 10−7, 3.78 × 10−6	4.13 × 10−12	1.10 × 10−43
10:5767177	rs76154345a	GDI2	4.43 × 10−6	7.80 × 10−11	-
10:111889779	rs11194997	MXI1	3.45 × 10−6	-	2.70 × 10−11
11:7543519	rs11041426	PPFIBP2	2.73 × 10−4	-	1.66 × 10−33
11:62203865	rs10897275	AHNAK	6.47 × 10−5	-	2.47 × 10−33
11:91616691	rs12225068	FAT3	3.80 × 10−5	-	6.48 × 10−10
13:76351286	rs474240	LMO7	2.53 × 10−4	-	9.28 × 10−9
13:114744546	rs75414584	RASA3	6.31 × 10−3	-	4.62 × 10−12
14:64390030	rs10873172a,d	SYNE2	6.29 × 10−8	5.95 × 10−13	6.47 × 10−27
14:69226931	rs11625064d	ZFP36L1	3.33 × 10−6	2.09 × 10−10	1.83 × 10−19
14:92795912	rs4904871	SLC24A4	2.06 × 10−4	-	2.15 × 10−278
14:103923475	rs2273699	MARK3	5.27 × 10−5	-	1.21 × 10−16
15:48400199	rs2675345	SLC24A5	4.92 × 10−3	-	1.09 × 10−9
16:54118132, 16:54131939	rs62034121, rs62034139a,e	FTO	1.16 × 10−9, 4.56 × 10−9	4.69 × 10−14	-
16:55322732	rs12930459a	IRX6	1.82 × 10−5	4.89 × 10−9	-

^aLocus previously reported as pleiotropically associated with cutaneous melanoma and nevus count, but not significant for cutaneous melanoma alone here.

^bLead SNP for Pigment (rs10434895) and nevus (rs10434895) are in LD r²_EUR = 1.0.

^cLead SNP for Pigment (rs520015) and nevus (rs593179) are in LD r²_EUR = 0.63.

^dSame lead SNP.

^eLead SNP for Pigment (rs62034121) and nevus (rs62034139) are in LD r²_EUR = 0.88.