1 Considering all SNPs regardless of genomic location

Here all SNPs are considered no matter where the SNP is located (within experimentally determined open chromatin region or not).

1.1 Deep learning (DeepSEA model)

type Annotation lead_causal lead_not_causal not_lead_causal not_lead_not_causal Enrichment.Pvalue Odds.Ratio Fold
control AoSMC 421 3612 29411 264866 0.182 1.050 1.044
control HFFMyc 402 3631 29430 264847 0.535 0.996 0.997
control HPF 432 3601 29400 264877 0.069 1.081 1.071
control RWPE1 426 3607 29406 264871 0.121 1.064 1.056
positive AdultCD4Th0 363 3670 29469 264808 0.985 0.889 0.900
positive CD20plus 365 3668 29467 264810 0.981 0.894 0.905
positive GM12878 385 3648 29447 264830 0.840 0.949 0.955
positive MonocytesCD14plusRO01746 413 3620 29419 264858 0.312 1.027 1.024

1.2 CADD Phred

type lead_causal lead_not_causal not_lead_causal not_lead_not_causal Enrichment.Pvalue Odds.Ratio Fold
CADD 37 3996 2277 292000 0.172 1.187 1.183

2 Considering SNPs that locate in open chromatin regions

Here we consider the SNPs that locate in corresponding open chromatin of certain cell types.

2.1 Without using any scores

type Annotation lead_causal lead_not_causal not_lead_causal not_lead_not_causal Enrichment.Pvalue Odds.Ratio Fold
control AoSMC 46 3987 3486 290791 0.621 0.962 0.963
control HFFMyc 53 3980 4713 289564 0.938 0.818 0.823
control HPF 40 3993 3278 290999 0.789 0.889 0.892
control RWPE1 35 3998 3077 291200 0.884 0.828 0.832
positive AdultCD4Th0 63 3970 3924 290353 0.119 1.174 1.169
positive CD20plus 44 3989 2066 292211 0.004 1.560 1.542
positive GM12878 52 3981 3563 290714 0.345 1.066 1.064
positive MonocytesCD14plusRO01746 38 3995 2915 291362 0.643 0.951 0.952

2.2 With CADD score

type Annotation lead_causal lead_not_causal not_lead_causal not_lead_not_causal Enrichment.Pvalue Odds.Ratio Fold
control AoSMC 8 4025 688 293589 0.724 0.848 0.850
control HFFMyc 9 4024 876 293401 0.845 0.749 0.752
control HPF 7 4026 708 293569 0.849 0.721 0.724
control RWPE1 6 4027 541 293736 0.749 0.809 0.811
positive AdultCD4Th0 10 4023 497 293780 0.153 1.469 1.459
positive CD20plus 9 4024 330 293947 0.043 1.992 1.964
positive GM12878 9 4024 534 293743 0.316 1.230 1.226
positive MonocytesCD14plusRO01746 5 4028 396 293881 0.632 0.921 0.922

2.3 With deep learning scores

type Annotation lead_causal lead_not_causal not_lead_causal not_lead_not_causal Enrichment.Pvalue Odds.Ratio Fold
control AoSMC 8 4025 435 293842 0.253 1.343 1.336
control HFFMyc 7 4026 623 293654 0.748 0.820 0.822
control HPF 6 4027 414 293863 0.502 1.058 1.057
control RWPE1 6 4027 503 293774 0.686 0.870 0.872
positive AdultCD4Th0 4 4029 486 293791 0.898 0.600 0.604
positive CD20plus 5 4028 345 293932 0.512 1.058 1.057
positive GM12878 7 4026 589 293688 0.696 0.867 0.869
positive MonocytesCD14plusRO01746 10 4023 516 293761 0.179 1.415 1.406

3 Summary

3.1 Odds ratio

3.2 Enrichment fold

The enrichment fold is defined as \(\frac{\Pr(\text{leading SNP} | \text{predicted causal SNP})}{\Pr(\text{predicted causal SNP})}\).