Table 1 Novel BCC loci identified in the European ancestry, Hispanic/Latino, and/or the multi-ancestry GWA meta-analyses.

From: Multi-ancestry genome-wide meta-analysis identifies novel basal cell carcinoma loci and shared genetic effects with squamous cell carcinoma

SNP

CHR

BP

Nearest gene(s)

EA/OA

OR (95%CI)

P

DE

I2 (Q)

rs56023437

1

38353403

INPP5B

T/C

0.96 (0.94,0.97)

4.51E-08

-,-,-,-

0 (0.7)

rs78663305

1

168497741

LOC100505918-XCL2

G/A

0.94 (0.92,0.96)

1.77E-08

-,-,-,-

0 (0.93)

rs6700380

1

214546861

PTPN14

T/C

0.95 (0.94,0.97)

2.50E-11

-,+,-,-

35.13 (0.2)

rs1254197

1

236361040

GPR137B

T/G

0.96 (0.94,0.97)

2.77E-08

-,N,-,-

0 (0.8)

rs6726950

2

10113496

GRHL1

G/A

1.07 (1.04,1.09)

9.97E-10

+,+,+,+

22.69 (0.27)

*rs1364689

2

34266792

MYADML-LOC100288911

A/G

1.65 (1.38,1.96)

2.32E-08

+,+

0 (0.63)

rs17479393

2

145653287

DKFZp686O1327

T/A

0.95 (0.93,0.97)

8.02E-10

-,-,-,-

17.07 (0.31)

rs10646896

2

173074802

DLX2-ITGA6

CTTT/C

0.94 (0.92,0.96)

8.73E-09

-,N,-,N

0 (0.84)

rs8176526

2

188345322

TFPI

T/C

1.05 (1.03,1.06)

1.41E-08

+,+,+,+

0 (0.73)

rs11684176

2

198954774

PLCL1

T/C

0.96 (0.95,0.98)

4.20E-08

-,-,-,-

0 (0.98)

*rs74269473

2

217359393

SMARCAL1-RPL37A

T/C

2.57 (1.85,3.57)

2.00E-08

+,+

36.75 (0.21)

rs11130229

3

50011540

RBM6

C/T

0.96 (0.95,0.97)

9.85E-09

-,-,-,-

0 (0.92)

rs4580527

3

101258778

FAM172BP-TRMT10C

C/A

0.95 (0.93,0.96)

6.71E-12

-,N,-,-

0 (0.97)

rs10936600

3

169514585

LRRC34

T/A

0.96 (0.94,0.97)

4.76E-08

-,-

0 (0.37)

rs13120159

4

186982959

SORBS2-TLR3

C/A

1.04 (1.03,1.06)

6.58E-09

+,+,+,+

0 (0.94)

rs11743151

5

38756717

MIR3650-OSMR

T/C

0.96 (0.95,0.97)

3.00E-08

-,+,-,-

48.02 (0.12)

rs76748680

5

52378850

ITGA2

G/GT

0.94 (0.93,0.96)

6.19E-10

-,N,-,N

0 (0.85)

rs1001114

5

73802976

ARHGEF28-ENC1

G/A

1.05 (1.03,1.06)

1.36E-08

+,+,+,+

0 (0.56)

rs2964574

5

151155711

G3BP1

A/G

1.05 (1.03,1.06)

8.07E-09

+,+,+,+

15.73 (0.31)

rs2237159

6

15388277

JARID2

A/G

1.04 (1.03,1.05)

3.87E-08

+,+,+,+

0 (0.67)

rs29243

6

29599102

GABBR1

A/G

1.2 (1.13,1.27)

1.53E-08

+,+,+,+

0 (0.94)

rs146968538

6

74499182

CD109

A/AT

0.95 (0.93,0.96)

6.50E-09

-,N,-,N

55.75 (0.13)

rs9388487

6

126678268

CENPW-RSPO3

T/G

0.95 (0.94,0.97)

1.23E-08

-,-,-,N

0 (0.58)

rs112108851

7

100359454

ZAN

T/C

0.95 (0.94,0.97)

6.05E-09

-,+,-,-

46.85 (0.13)

rs4871622

8

126618736

TRIB1-LOC100130231

T/C

0.96 (0.95,0.97)

4.43E-08

-,-

0 (0.49)

rs55807015

8

129003458

MIR1205-MIR1206

A/G

1.05 (1.04,1.07)

3.44E-11

+,+,+,+

0 (0.78)

rs9695995

9

92454643

UNQ6494-MIR4290

G/C

1.04 (1.03,1.06)

3.24E-08

+,+

0 (0.32)

rs2805831

9

100466636

XPA-FOXE1

A/G

0.94 (0.92,0.96)

7.06E-11

-,-,-,-

0 (0.57)

*rs74603527

11

99745220

CNTN5

G/A

3.53 (2.34,5.31)

1.66E-09

+,+

76.99 (0.037)

rs9668178

12

26421434

SSPN-ITPR2

A/T

1.05 (1.03,1.06)

3.71E-08

+,+,+,+

70.5 (0.02)

rs176265

12

120848516

MSI1-COX6A1

G/A

0.95 (0.93,0.97)

2.90E-08

-,-,-,-

0 (0.82)

rs12593917

15

49836867

FGF7-FAM227B

T/G

0.95 (0.94,0.97)

1.93E-10

-,-,-,-

0 (0.73)

rs7359174

15

67413837

SMAD3

A/G

1.07 (1.04,1.09)

7.49E-09

+,+,+,+

0 (0.74)

rs9910411

17

17609246

RAI1-SMCR5

T/G

1.04 (1.03,1.06)

1.62E-08

+,+,+,+

22 (0.28)

rs61494113

19

17401859

ANKLE1-ABHD8

A/G

1.05 (1.03,1.07)

4.25E-08

+,N,+,+

20.64 (0.28)

rs12833418

23

108593972

IRS4-GUCY2F

T/C

0.89 (0.86,0.93)

1.47E-10

-,N,-,-

44.43 (0.17)

  1. SNP single nucleotide polymorphism, Chr chromosome, Pos position build GRCh37, EA effect allele, OA other allele, OR odds ratio from fixed-effects summary estimates, CI confidence interval, DE direction of effect; direction is listed in order for GERA, MGB, UKB, and 23andMe (for the European ancestry BCC GWA meta-analysis); in order for GERA and MGB (for the Hispanic/Latino ancestry BCC GWA meta-analysis); or in order for European ancestry meta-analysis and Hispanic/Latino ancestry meta-analysis (for the multi-ancestry BCC GWA meta-analysis); N means not included in analysis; I2, heterogeneity index (0–100%); and Q, P-value for Cochrane’s Q statistic. Loci marked with a star * were identified in the Hispanic/Latino BCC GWA meta-analysis. We report the nearest gene(s) for each SNP; more complete annotation data (other genes within each locus) can be found in Supplementary Figs. 3 or 7.
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