Table 2.
Results of individual genotyping
| SNP | DNA pooling ranka |
P-values for allele frequencies differences | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| SNP identifier |
Geneb | Chrc | Position | Genotypingd | Replicatione | |||||
| All | M | F | All | M | F | |||||
| rs322239 | PTN | 7 | 136413862 | 12 | 4.8E–06 | 1.1E–04 | 5.7E–03 | 8.8E–01 | 7.4E–01 | 6.5E–01 |
| rs4841017 | 8 | 8614503 | 53 | 6.5E–06 | 2.3E–05 | 1.5E–02 | 2.3E–01 | 3.7E–01 | 4.1E–01 | |
| rs17385253 | 1 | 34564102 | 21 | 3.3E–05 | 7.7E–03 | 1.5E–03 | 2.8E–01 | 1.3E–01 | 8.5E–01 | |
| rs9329165f | 8 | 8614052 | 160 | 3.8E–05 | 3.0E–05 | 4.9E–02 | 2.1E–01 | 9.4E–01 | 9.5E–02 | |
| rs10483573 | 14 | 46932227 | 258 | 5.6E–05 | 3.6E–03 | 3.2E–03 | 6.1E–01 | 7.8E–01 | 3.9E–01 | |
| rs10504830 | CNBD1 | 8 | 88448321 | 115 | 1.1E–04 | 6.8E–04 | 2.2E–02 | 5.7E–01 | 1.4E–01 | 6.8E–01 |
| rs13290746g | 9 | 34858377 | 146 | 1.5E–04 | 3.6E–02 | 1.6E–03 | 3.8E–01 | 2.8E–01 | 7.8E–01 | |
| rs9959800 | 18 | 52115138 | 48 | 1.7E–04 | 1.1E–02 | 6.0E–03 | 1.4E–01 | 8.0E–01 | 3.8E–02 | |
| rs10797812 | 1 | 179716254 | 159 | 2.4E–04 | 2.2E–02 | 4.1E–03 | 5.1E–01 | 2.6E–01 | 7.2E–02 | |
| rs4875610 | CSMD1 | 8 | 3165318 | 430 | 4.1E–04 | 2.6E–02 | 6.3E–03 | 6.5E–01 | 4.7E–01 | 9.9E–01 |
| rs2123315f | 4 | 18642838 | 136 | 4.3E–04 | 2.0E–01 | 3.8E–03 | 9.6E–02 | 5.1E–01 | 1.3E–01 | |
| rs702543 | PDE4D | 5 | 58878531 | 184 | 8.2E–04 | 9.8E–04 | 9.5E–02 | 7.7E–04 | 2.7E–01 | 5.9E–04 |
| rs7666238 | 4 | 142453368 | 315 | 9.0E–04 | 2.1E–03 | 6.9E–02 | 6.1E–01 | 1.8E–01 | 7.9E–02 | |
| rs9431663 | TRIM67 | 1 | 227620956 | 211 | 1.2E–03 | 8.2E–01 | 1.2E–04 | 9.7E–01 | 8.6E–02 | 1.6E–01 |
| rs7594674g | 2 | 67191611 | 432 | 2.6E–03 | 4.3E–01 | 6.5E–04 | 3.9E–01 | 4.0E–01 | 7.9E–02 | |
| rs873989 | DAB1 | 1 | 58268619 | 148 | 3.5E–03 | 8.2E–01 | 1.3E–04 | 9.3E–01 | 4.9E–01 | 5.2E–01 |
| rs401897 | C20orf32 | 20 | 54463165 | 394 | 5.6E–03 | 6.5E–04 | 3.4E–01 | 5.2E–01 | 8.3E–01 | 4.4E–01 |
| rs201997 | ADAM18 | 8 | 39703325 | 186 | 6.4E–03 | 2.7E–04 | 5.3E–01 | 1.2E–01 | 6.0E–02 | 6.4E–01 |
| rs1452788 | TCF4 | 18 | 51268302 | 384 | 6.5E–03 | 6.7E–01 | 9.3E–04 | 5.7E–01 | 3.9E–01 | 9.7E–01 |
Abbreviation: SNPs, single-nucleotide polymorphisms.
SNPs within a copy number variation region are in bold.
a
Rank of SNPs based on log P results from the DNA pooling experiment.
b
SNP associate gene based on NCBI dbSNP.
c
Chromosome.
d
Results from individual genotyping the sample in the pools.
e
Results from genotyping the replication sample.
f
Genotyping distribution deviates from Hardy–Weinberg equilibrium in sample included in the pools (P-value < 0.0026).
g
Genotyping distribution deviates from Hardy–Weinberg equilibrium in both samples using two different SNP genotyping platforms (iPLEX and HME).