Table 3 Overview of fine-mapping results by region for regions 55–80 of the 80 regions fine-mapped, and summary results across all 80 regions

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

chr12:52773904-53816821

rs902774

0.9

3182 (553)

1

28 (1)

0 (0)

10

0.32 (0.28, 0.36)

chr13:73228139-74468916

rs9600079

0.9

3995 (888)

1

14 (5)

0 (0)

10

0.13 (0.11, 0.14)

chr14:52872330-53889699

rs8008270

0.9

2588 (410)

1

12 (2)

0 (0)

0

0.11 (0.10, 0.13)

chr14:68502988-69626744

rs7141529

0.9

3015 (822)

1

72 (17)

1 (1)

4

0.07 (0.02, 0.12)

chr14:70592256-71592256

rs8014671

0.6

2671 (139)

1

0 (0)

0 (0)

0

0.05 (0.02, 0.10)

chr17:118965-1119162

rs684232

0.9

3015 (848)

1

11 (4)

5 (3)

11

0.21 (0.19, 0.24)

chr17:35547276-36603565

rs11649743; rs4430796

0.9

1803 (444)

3

26 (10)

0 (0)

12

1.24 (1.10, 1.42)

chr17:46302314-47211374

rs138213197

0.9

2338 (521)

1

1 (1)

0 (0)

0

6.87 (4.24, 10.41)

chr17:47211375-47952263

rs11650494; rs7210100c

0.9

1319 (378)

1

83 (3)

0 (0)

24

0.07 (0.02, 0.14)

chr17:68608753-69617214

rs1859962

0.9

3138 (629)

1

24 (1)

0 (0)

20

0.79 (0.70, 0.89)

chr18:76270820-77273973

rs7241993

0.9

3097 (488)

1

3 (1)

0 (0)

0

0.16 (0.15, 0.19)

chr19:38235613-39244733

rs8102476

0.9

2472 (419)

1

18 (3)

9 (2)

16

0.27 (0.24, 0.31)

chr19:41485587-42485931

rs11672691

0.9

2119 (337)

1

4 (1)

0 (0)

1

0.19 (0.17, 0.22)

chr19:50840794-51864623

rs2735839

0.9

2300 (602)

3

21 (9)

3 (1)

8

0.86 (0.76, 0.98)

chr20:49027922-50027922

rs12480328

0.9

1839 (309)

1

44 (2)

0 (0)

37

0.08 (0.03, 0.13)

chr20:60515611-61515611

rs2427345

0.6

2943 (433)

1

17 (2)

8 (2)

0

0.04 (0.01, 0.09)

chr20:61862563-62874389

rs6062509

0.9

3157 (831)

1

21 (11)

6 (2)

2

0.16 (0.14, 0.18)

chr21:42401421-43401421

rs1041449

0.9

2177 (557)

1

31 (8)

20 (6)

7

0.20 (0.18, 0.23)

chr22:19257892-20257892

rs2238776

0.9

2092 (373)

1

1 (1)

0 (0)

0

0.08 (0.04, 0.13)

chr22:39952119-41297933

rs9623117

0.9

1978 (281)

1

55 (3)

0 (0)

6

0.11 (0.09, 0.13)

chr22:43000212-44013156

rs5759167

0.9

3466 (781)

2

18 (4)

6 (2)

5

0.76 (0.67, 0.87)

chrX:50741672-51741672

rs5945619

0.9

1087 (178)

1

94 (2)

1 (1)

93

1.20 (1.07, 1.37)

chrX:52396949-53396949

rs2807031

0.6

493 (22)

1

0 (0)

0 (0)

0

0.27 (0.11, 0.49)

chrX:66521550-67521550

rs5919432

0.75

1235 (111)

1

47 (1)

0 (0)

5

0.16 (0.08, 0.25)

chrX:69639850-70907983

rs4844289; rs6625711d

0.9

1274 (193)

1

69 (9)

1 (1)

24

0.17 (0.16, 0.20)

chrX:9314135-10314135

rs2405942

0.9

1973 (641)

1

11 (5)

1 (1)

7

0.16 (0.05, 0.32)

80 original GWAS loci

84 EUR original GWAS signals b

 

213,728 (38,745)

99

3700 (343)

1027 (127)

1155

30.30 (26.01, 35.89)

  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 Tables 1 and 2. Aggregated summary results across all of the 80 regions fine-mapped presented across Tables 1–3 are displayed in the final row of this table (in bold)
  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
  4. c African American signal rs7210100 had MAF=0.0015, P=0.31 in the European meta-analysis, but is situated proximal to rs11650494
  5. d SNP rs6625711 failed QC due to strongly discordant MAF between individual sub-studies within the meta-analysis and also between 1000 Genomes Phase1 and Phase3 cohorts (MAF in EUR 0.45 vs. 0.16) and is situated within the region boundary of rs4844289. Only a single signal within this region replicated in Europeans
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