Table 1 SNPs included in the pubertal development genetic risk score in the ProtecT study
SNP | Nearest gene (distance) | Chr | Positiona | Tanner stage decreasing/other allele | Tanner stage decreasing allele frequency (ProtecT controls)b | Tanner stage decreasing allele frequency (CEU) | Hardy–Weinberg equilibrium P value | Gene function |
|---|---|---|---|---|---|---|---|---|
rs2274465 | KDM4A | 1 | 44121557 | C/G | 0.664 | 0.676 | 0.9 | Histone demethylation |
rs6427782 | NR5A2 (+198Â kb) | 1 | 199798339 | A/G | 0.510 | 0.556 | 0.005 | DNA binding/steroid hormone receptor activity |
rs6762477 | RBM6 | 3 | 50093209 | A/G | 0.547 | 0.551 | 0.6 | Regulation of alternative splicing |
rs2153127 | LIN28B (+36Â kb) | 6 | 105348544 | T/C | 0.530 | 0.515 | 0.8 | Cell reprogramming |
rs7759938 | LIN28B (+6Â kb) | 6 | 105378954 | C/T | 0.318 | 0.373 | 1.0 | Cell reprogramming |
rs7821178 | PEX2 (–181 kb) | 8 | 78093837 | C/A | 0.665 | 0.658 | 0.1 | Peroxisome biogenesis |
rs10453225 | TMEM38B (–381 kb) | 9 | 108920220 | G/T | 0.681 | 0.700 | 0.2 | Maintenance of intracellular calcium release |
rs2090409 | TMEM38B (–428 kb) | 9 | 108967088 | C/A | 0.680 | 0.688 | 0.3 | Maintenance of intracellular calcium release |
rs10739221 | TMEM38B (–522 kb) | 9 | 109060830 | C/T | 0.772 | 0.770 | 0.5 | Maintenance of intracellular calcium release |
rs1324913 | KLF12 | 13 | 74635588 | T/G | 0.338 | 0.312 | 0.6 | Transcription factor/gene expression regulation |
rs12915845 | DET1 | 15 | 89042467 | C/T | 0.587 | 0.582 | 0.1 | Development regulation |
rs246185 | MKL2 (–35 kb) | 16 | 14395432 | C/T | 0.313 | 0.300 | 0.6 | Regulation of immediate early genes/muscle genes |
rs12446632 | GPRC5B (–38 kb) | 16 | 19935389 | A/G | 0.146 | 0.127 | 0.8 | Modulation of insulin secretion |