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Table 6 Putatively functional variants that correlate with our most significantly associated SNP, rs7538876, with an r2 > 0.9

From: Melanoma risk loci as determinants of melanoma recurrence and survival

SNP

Position

r2

Variant class

Gene

Putative function

rs7538876

1:17594950

-

intronic

PADI6

-

rs12132197

1:17596551

1

intronic

PADI6

TFBS (STAT1, STAT2)

rs12132237

1:17596699

1

intronic

PADI6

DNase I hypersensitivity cluster

     

TFBS (STAT1, STAT2)

rs7545115

1:17596918

1

intronic

PADI6

TFBS (STAT1, STAT2)

rs12134662

1:17597354

1

intronic

PADI6

TFBS (STAT1)

rs4920603

1:17599966

1

intronic

PADI6

DNase I hypersensitivity cluster

rs2526828

1:17602490

1

intergenic

-

DNase I hypersensitivity cluster

rs942457

1:17612173

1

exonic

RCC2

Synonymous

     

TFBS (INI1)

rs1324367

1:17625038

0.903

intronic

RCC2

TFBS (HEY1)

rs11577822

1:17627195

0.935

intronic

RCC2

DNase I hypersensitivity cluster

     

TFBS (HEY1)

rs1408420

1:17627402

0.935

intronic

RCC2

DNase I hypersensitivity cluster

     

TFBS (HEY1)

rs4920607

1:17632685

0.935

intronic

RCC2

H3K4me1 mark

     

TFBS (HEY1)

rs6586542

1:17636153

0.935

intronic

RCC2

H3K4me1 mark

     

DNase I hypersensitivity cluster

rs6675912

1:17641877

0.903

intergenic

-

H3K4me1 mark

  1. ENCODE database was used to establish transcription factor binding sites (TFBS), DNase I hypersensitivity clusters, and H3K4me1 chromatin marks. Variant annotation was performed using ANNOVAR.
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Journal of Translational Medicine

ISSN: 1479-5876

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