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. Author manuscript; available in PMC: 2020 Jul 1.
Published in final edited form as: Cancer Res. 2019 May 17;79(13):3192–3204. doi: 10.1158/0008-5472.CAN-18-3536

Table 2.

Nineteen gene expression-trait associations that may be at least partially explained by prostate cancer risk variants identified in previous GWAS or fine-mapping studies for genes located at genomic loci at least 500kb away from any GWAS-identified prostate cancer risk variants

Region Gene Model Typea Z score P valueb R2c Index SNP(s)d Distance to the
index SNP
(kb)		 P value after
adjusting for
index SNPse 		No. of SNPs in
prediction
models
1q21.2 RP11-353N4.4 Prostate lncRNA 4.74 2.19 × 10−6 0.03 rs17599629 981 0.009 58
1q21.3 RP11-98D18.3 Cross-Tissue lncRNA −4.81 1.48 × 10−6 0.01 rs17599629 1,078 2.87 × 10−6 12
2p11.2 TMSB10 Prostate Protein −4.88 1.08 × 10−6 0.04 rs2028900 634 0.67 29
2p15 MDH1 Cross-Tissue Protein 7.11 1.19 × 10−12 0.14 rs2430386 638 0.004 18
3q21.3 EFCAB12 Cross-Tissue Protein 4.73 2.28 × 10−6 0.09 rs13062436 903 0.008 129
3q25.2 DHX36 Prostate Protein −5.05 4.42 × 10−7 0.03 rs182314334 1,986 2.64 × 10−6 34
4q24 RP11-710F7.2 Prostate lncRNA 5.87 4.26 × 10−9 0.07 rs7679673 787 0.45 39
NPNT Prostate Protein 5.08 3.75 × 10−7 0.06 rs7679673 754 0.23 45
RP11-710F7.3 Prostate lncRNA 5.19 2.07 × 10−7 0.03 rs7679673 863 0.70 19
5p15.33 CTD-2589H19.6 Prostate lncRNA −5.52 3.32 × 10−8 0.22 rs2242652 603 2.37 × 10−4 68
6p24.2 GCNT6 Prostate Protein −5.32 1.06 × 10−7 0.03 rs4713266 572 7.16 × 10−4 2
7p14.1 MPLKIP Prostate Protein −6.52 7.16 × 10−11 0.26 rs17621345 701 0.18 49
10q11.22 RP11-38L15.3 Cross-Tissue lncRNA 4.74 2.10 × 10−6 0.01 rs76934034 868 3.36 × 10−6 36
12q13.13 RP1-288H2.2 Prostate transcript 11.55 7.67 × 10−31 0.01 rs902774 776 NA 4
RP1-288H2.4 Prostate lncRNA 11.53 8.97 × 10−31 0.04 rs902774 788 0.34 6
17q12 PIP4K2B Cross-Tissue Protein 4.90 9.78 × 10−7 0.02 rs11263763 818 0.40 5
CTC-268N12.2 Cross-Tissue lncRNA −4.78 1.75 × 10−6 0.04 rs8064454 692 0.12 28
19q13.12 CTD-3064H18.4 Cross-Tissue lncRNA 4.72 2.34 × 10−6 0.17 rs8102476 696 4.05 × 10−5 105
22q13.2 RBX1 Prostate Protein 5.12 3.08 × 10−7 0.03 rs11704314 549 0.36 18
a

Protein: protein coding genes; lncRNA: long non-coding RNAs; transcript: processed_transcript

b

P value: nominal p value from association analysis; the threshold after Bonferroni correction of 19,169 tests (0.05/19,169 =2.61×10−6) was used

c

R2: prediction performance (R2) derived using GTEx data; NA: not available

d

Risk SNPs identified in previous GWAS or fine-mapping studies. The risk SNP closest to the gene is presented. A full list of all risk SNPs, and their distances to the genes are presented in the Supplementary Table 3

e

using COJO method(40); all index SNPs in the corresponding region were adjusted for