Table 2 Overview of fine-mapping results by region for regions 28–54 of the 80 regions fine-mapped

From: Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants

Fine-mapping region boundary

Original index SNPs mapped

Pruning r2 threshold

SNPs (tags) analysed

Number of signals

Credible set SNPs (tags)

Credible set eQTL SNPs (tags)

Credible set SNPs P < 0.05 in AAsa

Region contribution to overall FRR of PrCab

chr6:116666036-117710052

rs339331

0.9

2981 (433)

1

102 (3)

0 (0)

101

0.18 (0.16, 0.20)

chr6:152932566-153941079

rs1933488

0.9

3636 (599)

1

86 (6)

45 (6)

20

0.12 (0.10, 0.14)

chr6:160081543-161382029

rs9364554

0.9

4101 (737)

3

151 (15)

65 (10)

7

1.03 (0.91, 1.19)

chr6:29573776-30573776

rs7767188

0.75

7085 (464)

1

606 (22)

372 (16)

13

0.07 (0.03, 0.11)

chr6:41036427-42043793

rs1983891

0.9

2840 (779)

1

33 (2)

9 (2)

33

0.18 (0.16, 0.21)

chr6:75995882-76995882

rs9443189

0.6

1966 (72)

1

0 (0)

0 (0)

0

0.06 (0.05, 0.07)

chr7:20494491-21496953

rs12155172

0.9

3170 (782)

1

4 (1)

0 (0)

2

0.16 (0.15, 0.19)

chr7:27091215-28476563

rs10486567

0.9

3372 (691)

1

11 (2)

1 (1)

3

0.34 (0.31, 0.39)

chr7:46937244-47937244

rs56232506

0.9

2803 (473)

1

53 (6)

0 (0)

34

0.08 (0.04, 0.13)

chr7:97307882-98316327

rs6465657

0.9

2892 (411)

1

31 (1)

11 (1)

0

0.27 (0.24, 0.31)

chr8:22938975-24028511

rs1512268; rs2928679

0.9

3507 (755)

2

74 (3)

1 (1)

16

0.77 (0.68, 0.87)

chr8:25392142-26410156

rs11135910

0.9

2836 (558)

1

4 (2)

0 (0)

0

0.07 (0.06, 0.09)

chr9:109651379-110656300

rs817826

0.75

2817 (547)

1

55 (1)

0 (0)

54

0.07 (0.04, 0.12)

chr9:21541998-22541998

rs17694493

0.9

2727 (615)

1

9 (3)

0 (0)

0

0.04 (0.02, 0.07)

chr10:103914221-104915094

rs3850699

0.75

1802 (154)

1

40 (2)

18 (2)

9

0.07 (0.03, 0.11)

chr10:122283141-123344709

rs2252004

0.9

3584 (928)

1

60 (7)

0 (0)

5

0.08 (0.04, 0.14)

chr10:126140936-127196872

rs4962416

0.6

3150 (324)

1

0 (0)

0 (0)

0

0.06 (0.02, 0.11)

chr10:45582985-46582985

rs76934034

0.9

1778 (124)

1

6 (2)

2 (1)

0

0.09 (0.04, 0.14)

chr10:51049496-52049496

rs10993994

0.9

741 (98)

1

1 (1)

0 (0)

1

1.44 (1.29, 1.64)

chr11:101901661-102901661

rs11568818

0.9

2368 (453)

1

2 (1)

0 (0)

2

0.17 (0.15, 0.19)

chr11:113307181-114307181

rs11214775

0.9

2197 (378)

1

2 (2)

1 (1)

1

0.10 (0.09, 0.12)

chr11:1733574-2734093

rs7127900

0.9

2808 (781)

1

40 (1)

17 (1)

40

0.66 (0.59, 0.75)

chr11:58415110-59610571

rs1938781

0.8

2506 (158)

1

1 (1)

0 (0)

0

0.13 (0.08, 0.18)

chr11:68484602-69953985

rs7931342

0.9

4274 (990)

2

44 (3)

0 (0)

44

0.85 (0.76, 0.97)

chr12:114185571-115584059

rs1270884

0.9

4980 (1309)

1

8 (3)

0 (0)

5

0.16 (0.14, 0.18)

chr12:47919618-48919618

rs80130819

0.6

2987 (187)

1

21 (2)

0 (0)

0

0.04 (0.01, 0.08)

chr12:49176010-50176010

rs10875943

0.9

1641 (319)

1

7 (3)

2 (2)

6

0.11 (0.09, 0.13)

  1. Published GWAS SNPs for which the signal or region replicated in our EUR meta-analysis are indicated, alongside the region co-ordinates assigned for fine-mapping analyses (GRCh37/hg19 assembly). The final priority pruner thresholds used and numbers of variants and priority pruner tags included in the analysis are shown. Summaries of the fine-mapping analysis results for each region contain the number of independent PrCa risk signals identified within each region, the size of the credible set of variants identified by JAM and the number of variants within the credible set that were also significantly associated eQTLs in TCGA PRAD data. As an additional category to assist variant prioritisation, the number of variants in the credible set that achieved a nominally significant P value threshold (P < 0.05) in an unconnected African Ancestry GWAS is indicated. The estimated contribution of each GWAS region to the overall familial relative risk of PrCa after fine-mapping is also provided. These results are a continuation from the regions displayed in Table 1 and results for all remaining regions fine-mapped are provided in Table 3
  2. a AAs African Ancestry population PrCa meta-analysis31
  3. b 84 of the 95 original GWAS signals identified in fine-mapping replicated in our EUR meta-analysis and were used when performing calculation of Familial Relative Risk of PrCa. rs2055109, rs7210100 and rs6625711 did not replicate in EUR but are situated within the region boundaries of other replicated signals, so were not excluded prior to fine-mapping. For five previously reported variants (rs7153648, rs12051443, rs636291, rs1571801 and rs103294), no variant within the region boundary replicated in the meta-analysis, and these regions were excluded prior to Bayesian analysis
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