Table 5 Risk loci for ER-negative breast cancer identified in the EUGENE gene-based analysis and not in previous GWAS

From: Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer

Locus Index

Gene

Chr

Start

N sentinel eQTL

Gene-based P-valuea

Sentinel eQTL with strongest association in adjusted GWAS

OncoScore

    

Tested

with P < 0.05 in adjusted GWAS*

 

Variant

P-valueb

 

1

INHBB

2

121103719

3

2

1.13E−07

rs6542583

5.37E−06

25.82

2

TNFSF10

3

172223298

4

3

4.93E−07

rs2041692

5.66E−07

86.01

3

VPS52

6

33218049

2

1

1.01E−06

rs17215231

2.73E−07

17.45

4

GTF2IRD2B

7

74508364

1

1

8.52E−07

rs2259337

8.52E−07

0

  1. aGene-based association P-value obtained when the EUGENE gene-based test was applied to the adjusted GWAS results
  2. bP-value in the Milne et al. GWAS3, adjusted for (i) the association with the sentinel risk variants identified in this study using the COJO-COND test; and (ii) the LD-score intercept
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