Table 2.
CCT-associated loci from meta-analysis of set 1 and set 2 samples
| Locusa | Chr. | Lead SNP | A1/A2 | Base pairg | Set 1–European samples (n = 13,057)
|
Set 2–Asian samples (n = 6,963)
|
Fisher’s method P | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AF1 | βc | s.e.c | P | AF1 | βc | s.e.c | P | ||||||
| COL8A2 | 1 | rs96067 | A/G | 36344507 | 0.80 | 0.03 | 0.02 | 4.1 × 10−2 | 0.58 | 0.11 | 0.02 | 2.3 × 10−11 | 2.7 × 10−11 |
| COL4A3 | 2 | rs7606754 | A/G | 227843424 | 0.35 | −0.07 | 0.01 | 3.4 × 10−7 | 0.36 | −0.07 | 0.02 | 1.3 × 10−4 | 1.1 × 10−9 |
| FNDC3B | 3 | rs4894535 | T/C | 173478299 | 0.17 | −0.10 | 0.02 | 9.0 × 10−8 | 0.27 | −0.09 | 0.02 | 1.9 × 10−6 | 5.1 × 10−12 |
| TBL1XR1-KCNMB2b | 3 | rs7620503 | T/C | 178786992 | 0.39 | −0.06 | 0.01 | 3.4 × 10−6 | 0.51 | −0.06 | 0.02 | 1.6 × 10−4 | 1.2 × 10−8 |
| NR3C2 | 4 | rs3931397 | T/G | 149298947 | 0.07 | −0.12 | 0.03 | 2.3 × 10−6 | 0.12 | −0.09 | 0.03 | 7.6 × 10−4 | 3.7 × 10−8 |
| ADAMTS6 | 5 | rs2307121 | T/C | 64661268 | 0.34 | 0.09 | 0.01 | 3.5 × 10−10 | 0.30 | 0.05 | 0.02 | 6.0 × 10−3 | 5.9 × 10−11 |
| FAM46A-IBTK | 6 | rs1538138 | T/C | 82851313 | 0.25 | −0.07 | 0.02 | 9.2 × 10−7 | 0.23 | −0.11 | 0.02 | 3.3 × 10−8 | 9.8 × 10−13 |
| VKORC1L1 | 7 | rs11763147 | A/G | 64964256 | 0.45 | 0.07 | 0.01 | 3.1 × 10−7 | 0.32 | 0.06 | 0.02 | 5.4 × 10−4 | 4.0 × 10−9 |
| C7orf42 | 7 | rs4718428 | T/G | 66058881 | 0.65 | 0.05 | 0.01 | 6.3 × 10−5 | 0.44 | 0.09 | 0.02 | 1.8 × 10−7 | 3.0 × 10−10 |
| MPDZ-NF1B | 9 | rs1324183 | A/C | 13547491 | 0.20 | −0.05 | 0.02 | 1.1 × 10−3 | 0.25 | −0.10 | 0.02 | 3.4 × 10−7 | 8.1 × 10−9 |
| LPAR1 | 9 | rs1007000 | T/C | 112702502 | 0.22 | 0.07 | 0.02 | 6.1 × 10−6 | 0.21 | 0.11 | 0.02 | 2.6 × 10−8 | 4.8 × 10−12 |
| RXRA-COL5A1d | 9 | rs1536482 | A/G | 136580349 | 0.34 | −0.12 | 0.01 | 6.3 × 10−19 | 0.34 | −0.08 | 0.02 | 8.9 × 10−6 | 3.0 × 10−22 |
| COL5A1 | 9 | rs7044529 | T/C | 136707872 | 0.15 | −0.13 | 0.02 | 1.1 × 10−11 | 0.20 | −0.05 | 0.02 | 1.4 × 10−2 | 4.8 × 10−12 |
| LCN12-PTGDS | 9 | rs11145951 | T/C | 138980085 | 0.49 | 0.09 | 0.01 | 9.2 × 10−12 | 0.69 | 0.04 | 0.02 | 2.3 × 10−2 | 6.4 × 10−12 |
| ARID5B | 10 | rs7090871 | T/C | 63500292 | 0.59 | 0.06 | 0.01 | 1.1 × 10−6 | 0.64 | 0.07 | 0.02 | 2.2 × 10−5 | 6.3 × 10−10 |
| ARHGAP20-POU2AF1 | 11 | rs4938174 | A/G | 110418450 | 0.31 | 0.06 | 0.01 | 4.3 × 10−5 | 0.15 | 0.11 | 0.02 | 3.5 × 10−6 | 3.6 × 10−9 |
| Near GLT8D2 (5′) | 12 | rs1564892 | A/G | 102969872 | 0.76 | −0.08 | 0.02 | 1.4 × 10−7 | 0.43 | −0.07 | 0.02 | 4.5 × 10−5 | 1.7 × 10−10 |
| FGF9-SGCGe | 13 | rs1034200 | A/C | 22126691 | 0.23 | 0.10 | 0.02 | 6.1 × 10−10 | 0.27 | 0.02 | 0.02 | 2.6 × 10−1 | 3.7 × 10−9 |
| Near FOXO1 (3′) | 13 | rs2721051 | T/C | 40008884 | 0.11 | −0.17 | 0.02 | 1.3 × 10−14 | 0.03 | −0.13 | 0.07 | 7.7 × 10−2 | 3.6 × 10−14 |
| Near TJP1 (5′) | 15 | rs785422 | T/C | 27961177 | 0.11 | −0.14 | 0.02 | 1.4 × 10−10 | 0.08 | −0.10 | 0.04 | 7.6 × 10−3 | 3.1 × 10−11 |
| SMAD3 | 15 | rs12913547 | T/C | 65254561 | 0.77 | −0.08 | 0.02 | 1.0 × 10−6 | 0.64 | −0.07 | 0.02 | 1.7 × 10−5 | 4.6 × 10−10 |
| Near AKAP13 (5′)f | 15 | rs6496932 | A/C | 83626571 | 0.20 | −0.11 | 0.02 | 6.8 × 10−11 | 0.36 | −0.06 | 0.02 | 3.1 × 10−4 | 6.7 × 10−13 |
| LRRK1 | 15 | rs930847 | T/G | 99376085 | 0.77 | −0.11 | 0.02 | 3.7 × 10−13 | 0.73 | −0.11 | 0.02 | 3.4 × 10−8 | 5.9 × 10−19 |
| CHSY1 | 15 | rs752092 | A/G | 99599457 | 0.66 | −0.08 | 0.01 | 5.9 × 10−9 | 0.78 | −0.05 | 0.02 | 1.7 × 10−2 | 2.4 × 10−9 |
| BANP-ZNF469 | 16 | rs9938149 | A/C | 86889141 | 0.62 | 0.17 | 0.01 | 6.8 × 10−37 | 0.74 | 0.16 | 0.02 | 3.1 × 10−15 | 2.4 × 10−49 |
| HS3ST3B1-PMP22 | 17 | rs12940030 | T/C | 14501741 | 0.71 | 0.08 | 0.01 | 5.7 × 10−8 | 0.54 | 0.06 | 0.02 | 5.1 × 10−4 | 7.4 × 10−10 |
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. Additional new loci for both European and Asian populations are shown in bold. The MPDZ-NF1B locus was previously reported as 9p23.
The lead SNP is within a validated non-coding mRNA, LINC00578.
Effect and s.e. are in standardized units.
An imputed SNP, rs3118516, in high LD with rs1536482 (complete LD in HapMap CEU set, r2 = 0.97 in the HapMap CHB and JPT set), has a lower association P value, with Fisher’s method P = 3.5 × 10−23.
An imputed SNP, rs9552680, in high LD with rs1034200 (r2 = 0.57 and 0.95 in HapMap CEU and CHB and JPT sets, respectively), has a lower association P value, with Fisher’s method P = 3.2 × 10−9.
An imputed SNP, rs10163187, in high LD with rs6496932 (r2 = 0.73 and 0.68 in HapMap CEU and CHB and JPT sets, respectively), has a lower association P value, with Fisher’s method P = 1.7 × 10−13.
Genomic positions are based on NCBI Build 36/hg18.