Table 4.
SNPs associated with TSC, TY and TSY in the QUEST population (n = 264)
| SNP name | SNP alleles phu/tbr | Chromosome | Minor allele frequencya | TSC (R2)b | TY (R2)b | TSY (R2)b | SNP differential in case-control population for |
|---|---|---|---|---|---|---|---|
| ADXR_SNP5705 (5710) c | T/C | I | 0.491 (C) | ns | * (2.0) ↑ | ** (3.5) ↑ | TY, TSY, TSC |
| CP5_SNP3041 | C/T | II | 0.442 (C) | *** (5.1) ↑ | ns | ns | TSC, TY |
| FBA_SNP_c2_11924 | C/T | V | 0.103 (T) | ** (3.0) ↑ | * (1.4) ↑ | ** (3.8) ↑ | TSC |
| CP12.1_SNP_c2_54011 | C/T | VI | 0.082 (T) | ns | ** (3.1) ↓ | * (2.1) ↓ | TY, TSY, TSC |
| MAK_SNP7832 (7475, 7634 7588) | T/C | VI | 0.467 (T) | ns | *** (5.0) ↓ | ** (3.5) ↓ | TY, TSY |
| MAK_SNP7576 | G/A | VI | 0.491 (A) | ns | *** (4.6) ↓ | *** (5.9) ↓ | TSC, TY, TSY |
| MAK_SNP7884 | A/C | VI | 0.113 (A) | ns | ** (2.8) ↑ | * (1.5) ↑ | novel |
| QUA1_SNP_c2_9204 | G/A | VI | 0.452 (G) | ns | ** (2.7) ↓ | * (1.8) - | novel |
| QUA1_SNP9502 | G/A | VI | 0.070 (G) | ns | ** (3.3) ↑ | * (1.8) - | novel |
| QUA1_SNP_c2_9203 | C/G | VI | 0.453 (C) | ns | ** (3.0) ↓ | * (2.2) - | TY, TSY |
| PPR_SNP7181 | T/C | IX | 0.495 (C) | *** (4.8) ↑ | ns | ns | TSC, TY |
| PPR_SNP7037 (7077) | C/T | IX | 0.440 (T) | ** (3.1) ↑ | ns | ns | TSC, TY |
| PPR_SNP7083 | A/G | IX | 0.318 (G) | ** (2.2) - | ns | ns | TSC, TY |
| RP60S_SNP_c2_3063 | T/C | IX | 0.157 (T) | * (1.3) ↑ | * (2.0) ↑ | ** (3.9) ↑ | TY, TSY |
| CIS_SNP4479 | C/G | XII | 0.438 (C) | *** (4.2) ↓ | ns | ns | novel |
Associations of SNPs with a minimum minor allele frequency of 1% and at least one association at p < 0.01 are shown
aThe minor frequency allele is shown in parenthesis
bns = not significant at α =0.05; * significant at α = 0.05, ** significant at α = 0.01, *** significant at α = 0.001; Arrows indicate the effect of the minor frequency SNP allele on the trait compared to the population mean: ↑ increasing, ↓ decreasing, − ambiguous
cNumbers in parenthesis identify SNPs in nearly complete LD that showed similar associations