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. Author manuscript; available in PMC: 2014 Feb 1.
Published in final edited form as: Nat Genet. 2013 Jan 6;45(2):155–163. doi: 10.1038/ng.2506

Table 1.

CCT-associated loci from meta-analysis of set 1 samples (13,057 individuals of European descendant unaffected with eye disease)

Locusa,b Chr. Lead SNP Base paire A1/A2 AF1 Discovery set (n = 9,584)
Australian and UK twins (n = 3,473 from 1,905 families)
Combined set 1 (n = 13,057 individuals)
Conditional and joint analysis
β (s.e.)d P β (s.e.)d P β (s.e.)d P I2 Phet β (s.e.)d P
USP37 2 rs10189064 219035744 A/G 0.04 −0.19 (0.05) 5.9 × 10−5 −0.30 (0.07) 1.8 × 10−5 −0.23 (0.04) 1.0 × 10−8 30.2 0.15 −0.23 (0.04) 1.1 × 10−8
GPR15 3 rs3749260 99733552 A/C 0.13 −0.12 (0.02) 9.5 × 10−7 −0.11 (0.04) 3.8 × 10−3 −0.12 (0.02) 1.3 × 10−8 0 0.94 −0.12 (0.02) 1.2 × 10−8
TIPARPc 3 rs9822953 157954765 T/C 0.67 0.08 (0.02) 7.5 × 10−7 0.07 (0.03) 1.1 × 10−2 0.08 (0.01) 2.7 × 10−8 0 0.69 0.08 (0.01) 3.0 × 10−8
CWC27- ADAMTS6 5 rs1117707 64425421 A/G 0.70 −0.11 (0.02) 2.8 × 10−10 −0.06 (0.03) 4.0 × 10−2 −0.09 (0.01) 8.4 × 10−11 0 0.75 −0.09 (0.02) 9.0 × 10−11
RXRA- COL5A1b 9 rs3118520 136581416 A/G 0.63 0.14 (0.02) 1.3 × 10−18 0.09 (0.03) 1.5 × 10−3 0.13 (0.01) 3.4 × 10−20 12.1 0.33 0.13 (0.01) 5.2 × 10−21
COL5A1b 9 rs7044529 136707872 T/C 0.15 −0.12 (0.02) 1.5 × 10−−8 −0.14 (0.04) 1.5 × 10−4 −0.13 (0.02) 1.1 × 10−11 0 0.61 −0.13 (0.02) 9.4 × 10−12
LCN12- PTGDS 9 rs11145951 138980085 T/C 0.49 0.09 (0.01) 1.4 × 10−9 0.08 (0.03) 1.7 × 10−3 0.09 (0.01) 9.2 × 10−12 0 0.6 0.09 (0.01) 1.1 × 10−11
FGF9-SGCG 13 rs1034200 22126691 A/C 0.23 0.09 (0.02) 6.4 × 10−7 0.12 (0.03) 1.8 × 10−4 0.10 (0.02) 6.1 × 10−10 31.6 0.12 0.09 (0.01) 5.4 × 10−10
Near FOXO1 (3′) 13 rs2721051 40008884 T/C 0.11 −0.15 (0.02) 1.4 × 10−9 −0.22 (0.04) 6.8 × 10−7 −0.17 (0.02) 1.3 × 10−14 10.9 0.33 −0.17 (0.02) 1.6 × 10−14
Near TJP1 (5′) 15 rs785422 27961177 T/C 0.11 −0.14 (0.02) 1.8 × 10−8 −0.13 (0.04) 2.1 × 10−3 −0.14 (0.02) 1.4 × 10−10 33.1 0.1 −0.14 (0.02) 1.5 × 10−10
Near AKAP13 (5′) 15 rs6496932 83626571 A/C 0.20 −0.09 (0.02) 4.1 × 10−7 −0.15 (0.03) 1.2 × 10−5 −0.11 (0.02) 6.8 × 10−11 0 0.97 −0.11 (0.02) 6.7 × 10−11
LRRK1b 15 rs2034809 99372922 A/G 0.50 −0.05 (0.02) 5.2 × 10−4 −0.05 (0.03) 5.7 × 10−2 −0.05 (0.01) 7.5 × 10−5 0 0.89 −0.08 (0.01) 2.4 × 10−8
LRRK1b 15 rs930847 99376085 T/G 0.77 −0.12 (0.02) 3.2 × 10−11 −0.10 (0.03) 2.8 × 10−3 −0.11 (0.02) 3.7 × 10−13 0 0.9 −0.13 (0.02) 4.0 × 10−16
CHSY1b 15 rs752092 99599457 A/G 0.66 −0.08 (0.02) 4.7 × 10−8 −0.06 (0.03) 3.4 × 10−2 −0.08 (0.01) 5.9 × 10−9 44.3 0.03 −0.09 (0.01) 5.7 × 10−10
BANP- ZNF469 16 rs6540223 86878937 T/C 0.64 0.19 (0.02) 3.0 × 10−31 0.18 (0.03) 5.8 × 10−10 0.18 (0.01) 1.3 × 10−39 22.5 0.22 0.18 (0.01) 5.9 × 10−39
HS3ST3B1- PMP22 17 rs2323457 14494915 A/C 0.29 −0.07 (0.02) 6.0 × 10−6 −0.09 (0.03) 1.9 × 10−3 −0.08 (0.01) 4.7 × 10−8 0 0.48 −0.08 (0.01) 5.4 × 10−08

Chr., chromosome; A1/A2, reference allele/other allele; AF, allele frequency; s.e., standard error.

a

Locus assigned to the RefSeq protein-coding gene within or near the association signal interval (defined by LD plot using the measure r2 > 0.9 with the lead SNP implemented in SNAP using the CEU reference). The locus was assigned to the interval defined by the two flanking RefSeq protein-coding genes if clearly intergenic. New loci for European populations are shown in bold. The FGF9-SGCG locus was previously reported as AVGR8.

b

These loci contain multiple independent associations, as suggested from the results of the conditional and joint analysis.

c

The lead SNP is within a validated non-coding mRNA, LOC730091.

d

Effect and s.e. are in standardized units.

e

Genomic positions are based on NCBI Build 36/hg18.