Table 3.
Comparison with previously reported SNPs associated with CCT
| Previously Reported |
Latinos |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP ID | Chr | Position | Genes Nearby | Effect | Freq | β | Reference(s) | A1/A2 | AF1 | β | P | Imputed | Consistency of Direction |
| Allele | |||||||||||||
| rs3767703 | 1 | 36555758 | COL8A2 | −4.43 | (19) | C/T | 0.93 | −0.03 | 9.81E-01 | NA | |||
| rs7550047 | 1 | 36567343 | COL8A2 | −4.42 | (19) | A/G | 0.91 | 0.88 | 5.00E-01 | Y | NA | ||
| rs96067 | 1 | 36571920 | COL8A2 | −4.80 | (19) | G/A | 0.38 | −1.15 | 1.29E-01 | NA | |||
| rs10189064 | 2 | 219327500 | USP37 | A/G | 0.04 | −0.19 | (23) | A/G | - | - | - | NA | NA |
| rs7606754 | 2 | 228135180 | COL4A3 | A/G | 0.35 | −0.07 | (23) | A/G | 0.41 | −0.79 | 2.91E-01 | Y | Y |
| rs3749260 | 3 | 98250862 | GPR15 | A/C | 0.13 | −0.12 | (23) | A/C | 0.14 | 1.76 | 1.12E-01 | Y | N |
| rs9822953 | 3 | 156472071 | TIPARP | T/C | 0.67 | 0.08 | (23) | T/C | 0.74 | 1.81 | 3.51E-02 | Y | Y |
| rs4894535 | 3 | 171995605 | FNDC3B | T/C | 0.17 | −0.10 | (23) | T/C | 0.25 | −2.16 | 1.09E-02 | Y | |
| rs7620503 | 3 | 177304298 | TBL1XR1-KCNMB2 | T/C | 0.39 | −0.06 | (23) | T/C | 0.44 | −1.18 | 1.16E-01 | Y | Y |
| rs3931397 | 4 | 149079497 | NR3C2 | T/G | 0.07 | −0.12 | (23) | T/G | 0.06 | −6.77 | 1.28E-05 | Y | Y |
| rs1117707 | 5 | 64389665 | CWC27-ADAMTS6 | A/G | 0.7 | −0.11 | (23) | A/G | 0.55 | −0.59 | 4.26E-01 | Y | Y |
| rs1538138 | 6 | 82794594 | IBTK | T | 0.18–0.30 | −4.23 | (17) | T/C | 0.14 | −3.53 | 7.16E-04 | Y | |
| rs11763147 | 7 | 65326821 | VKORC1L1 | A/G | 0.45 | 0.07 | (23) | A/G | 0.45 | 1.62 | 2.85E-02 | Y | |
| rs4718428 | 7 | 66421446 | C7orf42 | G | 0.46–0.74 | −3.18 | (17) | G/T | 0.45 | −2.89 | 1.89E-04 | Y | Y |
| rs1324183 | 9 | 13557491 | 9p23 | A | 0.21–0.27 | −3.37 | (17) | A/C | 0.14 | −2.86 | 1.15E-02 | Y | Y |
| rs1007000 | 9 | 113662681 | LPAR1 | T/C | 0.22 | 0.07 | (23) | T/C | 0.30 | 3.43 | 1.62E-05 | Y | |
| rs1409832 | 9 | 137428425 | RXRA-COL5A1 | −3.95 | (19) | T/G | 0.76 | 4.32 | 7.11E-07 | NA | |||
| rs4842044 | 9 | 137431904 | RXRA-COL5A1 | −4.67 | (19) | C/T | 0.47 | −4.14 | 2.25E-08 | Y | NA | ||
| rs1536478 | 9 | 137432248 | RXRA-COL5A1 | −4.63 | (19) | G/A | 0.47 | −4.17 | 2.03E-08 | Y | NA | ||
| rs3118516 | 9 | 137439792 | RXRA-COL5A1 | A | 0.34 | −0.15 | (21) | A/G | 0.26 | −4.91 | 5.89E-07 | Y* | Y |
| rs3132306 | 9 | 137440212 | RXRA-COL5A1 | T | 0.66 | 0.15 | (21) | T/C | 0.72 | 4.83 | 7.63E-07 | Y* | Y |
| rs1536482 | 9 | 137440528 | RXRA-COL5A1 | G | 0.34 | 0.22 | (18),(21) (A, Freq | G/A | 0.71 | 5.21 | 5.47E-08 | Y* | Y |
| = 0.33, β = −0.15) | |||||||||||||
| rs7044529 | 9 | 137568051 | COL5A1 | (19) | C/T | 0.78 | 3.23 | 2.58E-04 | NA | ||||
| rs11145951 | 9 | 139860264 | LCN12-PTGDS | T/C | 0.49 | 0.09 | (23) | T/C | 0.44 | 3.26 | 1.15E-05 | Y | |
| rs7090871 | 10 | 63830286 | ARID5B | T/C | 0.59 | 0.06 | (23) | T/C | 0.71 | 1.40 | 8.75E-02 | Y | Y |
| rs1006368 | 10 | 126346603 | FAM53B | A/G | (20) | C/T | 0.80 | −2.01 | 2.59E-02 | Y | NA | ||
| rs11245330 | 10 | 126380338 | FAM53B | A/G | (20) | A/G | 0.20 | 2.10 | 1.96E-02 | NA | |||
| rs4938174 | 11 | 110913240 | ARHGAP20-POU2AF1 | A/G | 0.31 | 0.06 | (23) | A/G | 0.20 | 3.34 | 2.97E-04 | Y | |
| rs1564892 | 12 | 104445742 | Near GLT8D2 (5') | A/G | 0.76 | −0.08 | (23) | A/G | 0.74 | −0.37 | 6.66E-01 | Y | Y |
| rs1034200 | 13 | 23228691 | FGF9-FTHL7 | 0.14 | (18) | C/A | 0.75 | −1.69 | 5.06E-02 | NA | |||
| rs2755237 | 13 | 41109429 | FOXO1 | A/C | (20) | A/C | 0.86 | 3.62 | 6.45E-04 | NA | |||
| rs2721051 | 13 | 41110884 | FOXO1 | A/G | (20) | C/T | 0.92 | 4.24 | 1.89E-03 | NA | |||
| rs785422 | 15 | 30173885 | Near TJP1 (5') | T/C | 0.11 | −0.14 | (23) | T/C | 0.07 | −3.24 | 2.66E-02 | Y | |
| rs12913547 | 15 | 67467507 | SMAD3 | T/C | 0.77 | −0.08 | (23) | T/C | 0.71 | −0.44 | 5.87E-01 | Y | |
| rs6496932 | 15 | 85825567 | PDE8A-AKAP13 | 0.13 | (18) | C/A | 0.77 | 1.53 | 8.32E-02 | NA | |||
| rs1828481 | 15 | 85840912 | AKAP13 | C | 0.45–0.56 | 3.12 | (17) | C/A | 0.49 | 1.88 | 1.21E-02 | Y | NA |
| rs7172789 | 15 | 85843517 | AKAP13 | C | 0.45–0.56 | 3.14 | (17) | C/T | 0.48 | 1.72 | 2.14E-02 | Y | |
| rs930847 | 15 | 101558562 | LRRK1 | G | 0.17–0.39 | 3.72 | (17) | G/T | 0.19 | 3.97 | 2.79E-05 | Y | |
| rs4965359 | 15 | 101585336 | LRRK1 | A | 0.40–0.67 | −3.50 | (17) | A/G | 0.54 | −3.77 | 4.32E-07 | Y | Y |
| rs12447690 | 16 | 88298124 | ZNF469 | T/C | 0.17 | (20),(19),(18) (G, | T/C | 0.64 | 4.14 | 1.18E-07 | Y | ||
| β = −0.18), (21) (T, Freq = 0.64, β = 0.16) | |||||||||||||
| rs7500824 | 16 | 88299491 | ZNF469 | A | 0.36 | −0.16 | (21) | A/G | 0.24 | −4.70 | 6.35E-07 | Y | Y |
| rs7405095 | 16 | 88307825 | ZNF469 | A | 0.36 | −0.16 | (21) | A/G | 0.20 | −6.02 | 1.87E-07 | Y* | Y |
| rs7501109 | 16 | 88320862 | ZNF469 | C | 0.64 | 0.16 | (21) | C/G | 0.80 | 4.95 | 2.15E-06 | Y* | Y |
| rs7501402 | 16 | 88320911 | ZNF469 | A | 0.36 | −0.16 | (21) | A/T | 0.36 | −4.38 | 2.94E-07 | Y | Y |
| rs6540223 | 16 | 88321436 | ZNF469 | T | 0.64 | 0.16 | (21) | T/C | 0.80 | 4.96 | 2.22E-06 | Y* | Y |
| rs12448211 | 16 | 88330513 | ZNF469 | A | 0.62 | 0.16 | (21) | A/G | 0.65 | 4.51 | 3.89E-08 | Y | Y |
| rs9938149 | 16 | 88331640 | ZNF469 | A/C | (20),(19),(21) (A, | A/C | 0.79 | 4.56 | 3.62E-07 | Y | |||
| Freq = 0.62, β = 0.16) | |||||||||||||
| rs9922572 | 16 | 88334112 | ZNF469 | A | 0.34 | −0.14 | (21) | A/C | 0.20 | −4.82 | 2.01E-06 | Y | Y |
| rs9925231 | 16 | 88338107 | ZNF469 | −4.79 | (19) | T/C | 0.33 | −4.37 | 4.33E-07 | Y | NA | ||
| rs7204132 | 16 | 88344517 | ZNF469 | −4.95 | (19) | T/G | 0.18 | −4.32 | 4.35E-05 | Y | NA | ||
| rs9927272 | 16 | 88346709 | ZNF469 | −3.95 | (19) | G/A | 0.34 | −2.72 | 5.68E-04 | NA | |||
| rs2323457 | 17 | 14554190 | HS3ST3B1-PMP22 | A/C | 0.29 | −0.07 | (23) | A/C | 0.40 | −0.89 | 2.32E-01 | Y | Y |
Abbreviations: Chr, chromosome; Freq, frequency; A1/A2, allele 1/allele 2. For previously reported SNPs with multiple references, additional information on the allele, frequency, and effect size is given in parentheses. For this Latino population, the frequency for allele 1 is given and is modeled as the effect allele. The program simpleM was used as a multiple testing correction method for correlated SNPs, identifying 40 independent tests and thus, giving a Bonferroni correction P value of 0.05/40 = 0.00125. P values meeting this threshold are shown in bold. The direction of effect was consistent for most SNPs, except rs3749260. SNP positions are according to GRCh37/hg19.
*SNPs with suboptimal Rsq (0.62 < Rsq < 0.78).