Skip to main content
. 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 3.

Testing CCT-associated loci for susceptibility to keratoconus and POAG

Locusb Chr. Lead SNP A1/A2 OR (95% CI)a Pc Effect direction as expected?d OR (95% CI)a Pc Effect direction as expected?d
COL8A2 1 rs96067 A/G 0.91 (0.80–1.04) 0.16 + 0.98 (0.89–1.08) 0.64 +
COL4A3 2 rs7606754 A/G 1.19 (1.05–1.35) 6.0 × 10−3 + 0.96 (0.89–1.05) 0.38 −
FNDC3B 3 rs4894535 T/C 1.47 (1.29–1.68) 4.9 × 10−9 + 0.83 (0.74–0.92) 5.6 × 10−4 −
TBL1XR1-KCNMB2 3 rs7620503 T/C NAe NAe NAe 0.91 (0.84–0.98) 0.02 −
NR3C2 4 rs3931397 T/G 1.20 (1.00–1.44) 0.05 + 0.90 (0.78–1.05) 0.17 −
ADAMTS6 5 rs2307121 T/C 1.01 (0.90–1.12) 0.91 − 0.94 (0.87–1.02) 0.12 +
FAM46A-IBTK 6 rs1538138 T/C 1.06 (0.94–1.19) 0.37 + 0.99 (0.90–1.07) 0.74 −
VKORC1L1 7 rs11763147 A/G 1.19 (0.97–1.46) 0.09 − 1.07 (0.97–1.18) 0.16 −
C7orf42 7 rs4718428 T/G 1.25 (1.01–1.54) 0.04 − 1.01 (0.93–1.10) 0.80 −
MPDZ-NF1B 9 rs1324183 A/C 1.33 (1.18–1.51) 5.2 × 10−6 + 1.07 (0.97–1.18) 0.16 +
LPAR1 9 rs1007000 T/C 0.89 (0.78–1.02) 0.08 + 0.99 (0.90–1.09) 0.87 +
RXRA-COL5A1 9 rs1536482 A/G 1.32 (1.19–1.47) 2.6 × 10−7 + 1.00 (0.92–1.09) 0.94 +
COL5A1 9 rs7044529 T/C 1.37 (1.19–1.57) 8.0 × 10−6 + 0.98 (0.88–1.10) 0.77 −
LCN12-PTGDS 9 rs11145951 T/C 0.86 (0.78–0.96) 5.8 × 10−3 + 1.02 (0.94–1.10) 0.72 −
ARID5B 10 rs7090871 T/C 1.05 (0.94–1.17) 0.36 − 1.00 (0.92–1.09) 0.96 −
ARHGAP20-POU2AF1 11 rs4938174 A/G 0.89 (0.80–1.00) 0.06 + 0.92 (0.85–1.00) 0.06 +
Near GLT8D2 (5′) 12 rs1564892 A/G NAe NAe NAe 1.24 (1.06–1.45) 6.7 × 10−3 +
FGF9-SGCG 13 rs1034200 A/C 1.07 (0.93–1.22) 0.33 − 0.96 (0.88–1.04) 0.34 +
Near FOXO1 (3′) 13 rs2721051 T/C 1.62 (1.40–1.88) 2.7 × 10−10 + 1.08 (0.95–1.22) 0.24 +
Near TJP1 (5′) 15 rs785422 T/C 0.93 (0.78–1.11) 0.42 − 1.05 (0.93–1.18) 0.46 +
SMAD3 15 rs12913547 T/C 1.18 (1.01–1.38) 0.03 + 1.00 (0.92–1.10) 0.95 +
Near AKAP13 (5′) 15 rs6496932 A/C 1.06 (0.83–1.35) 0.63 + 1.00 (0.91–1.11) 0.94 +
LRRK1 15 rs930847 T/G 0.96 (0.83–1.11) 0.55 − 0.99 (0.91–1.09) 0.89 −
CHSY1 15 rs752092 A/G 0.98 (0.86–1.12) 0.81 − 1.03 (0.95–1.11) 0.53 +
BANP-ZNF469 16 rs9938149 A/C 1.25 (1.11–1.40) 1.9 × 10−4 − 1.02 (0.93–1.13) 0.63 −
HS3ST3B1-PMP22 17 rs12940030 T/C 0.99 (0.87–1.14) 0.92 + 1.04 0.39 −
a

Study-specific results are given in supplementary tables 11 and 12.

b

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.

c

P values that are significant after correction for multiple testing (P < 0.001 for testing 26 independent SNPs in 2 diseases) are shown in bold.

d

Given the association between reduced CCT and elevated keratoconus or glaucoma risk, it is expected that the CCT-reducing allele is the keratoconus or POAG risk allele.

+, the effect direction is as expected; −, the effect direction is not as expected.

e

SNPs were not genotyped in the two keratoconus case-control studies and are therefore presented as missing values (NA).