Table 1 Odds ratios of sampling and permutations for two datasets
| Â | Sampling | Permutations | ||||
|---|---|---|---|---|---|---|
| Â | Significantly associated SNPs | Significantly associated SNPs | Suggestively associated SNPs | |||
| Â | OR [95% CI] | P-value | OR [95% CI] | P-value | OR [95% CI] | P-value |
| Â | Â | Genic and regulatory features | Â | Â | Â | |
TSS 1 kb upstream | 3.23 [2.42-4.31] | 3.25 × 10 -17 | 2.86 [2.10-3.97] | <5.00 × 10 -05 | 1.25 [1.01-1.60] | 1.94 × 10 -02 |
TSS 5 kb upstream | 3.24 [2.69-3.91] | 1.56 × 10 -38 | 3.01 [2.41-3.76] | <5.00 × 10 -05 | 1.24 [1.08-1.44] | 9.00 × 10 -04 |
CpG Islands | 3.69 [2.49-5.47] | 2.09 × 10 -12 | 3.03 [2.10-4.70] | <5.00 × 10 -05 | 1.05 [0.79-1.49] | 4.05 × 10 -01 |
ORegAnno | 2.69 [1.85-3.90] | 6.24 × 10 -08 | 2.58 [1.86-3.85] | <5.00 × 10 -05 | 1.37 [1.05-1.91] | 8.40 × 10 -03 |
vega Genes | 2.08 [1.83-2.37] | 1.84 × 10 -29 | 1.98 [1.70-2.31] | <5.00 × 10 -05 | 1.17 [1.08-1.28] | 5.00 × 10 -05 |
OMIM Genes | 2.62 [2.30-2.98] | 1.35 × 10 -48 | 2.51 [2.13-2.97] | <5.00 × 10 -05 | 1.24 [1.13-1.35] | <5.00 × 10 -05 |
OMIM Morbid Regions | 4.33 [3.57-5.25] | 5.95 × 10 -58 | 4.24 [3.20-5.75] | <5.00 × 10 -05 | 1.38 [1.18-1.62] | <5.00 × 10 -05 |
Exons | 4.09 [3.34-5.01] | 5.35 × 10 -49 | 3.67 [2.94-4.62] | <5.00 × 10 -05 | 1.39 [1.20-1.65] | <5.00 × 10 -05 |
Intronic SNPs | 2.02 [1.78-2.30] | 1.92 × 10 -27 | 1.92 [1.63-2.25] | <5.00 × 10 -05 | 1.15 [1.06-1.26] | 3.00 × 10 -05 |
Non-Syn. SNPs | 4.26 [3.26-5.57] | 2.24 × 10 -31 | 3.78 [2.90-5.17] | <5.00 × 10 -05 | 1.37 [1.12-1.70] | 7.00 × 10 -04 |
Coding SNPs | 3.94 [3.15-4.92] | 1.73 × 10 -38 | 3.52 [2.78-4.55] | <5.00 × 10 -05 | 1.37 [1.16-1.63] | 5.00 × 10 -05 |
Syn. SNPs | 3.15 [2.32-4.28] | 6.45 × 10 -15 | 2.81 [2.10-3.94] | <5.00 × 10 -05 | 1.24 [1.00-1.59] | 3.09 × 10 -02 |
Gained Stops | 8.42 [1.17-60.53] | 1.04 × 10 -02 | 8.17 [2.26-Infinity] | 9.50 × 10 -04 | 4.74 [1.50-Infinity] | 2.10 × 10 -03 |
3′UTR | 3.24 [2.46-4.26] | 2.69 × 10 -19 | 2.92 [2.26-3.92] | <5.00 × 10 -05 | 1.29 [1.07-1.61] | 4.75 × 10 -03 |
5′UTR | 2.97 [1.70-5.19] | 5.08 × 10 -05 | 2.45 [1.56-4.90] | 5.00 × 10 -05 | 1.37 [0.97-2.30] | 5.71 × 10 -02 |
RNA Genes | 1.74 [0.52-5.85] | 3.80 × 10 -01 | 1.46 [0.64-7.02] | 2.25 × 10 -01 | 0.50 [0.27-1.50] | 6.21 × 10 -02 |
ncRNA | 1.62 [0.86-3.04] | 1.57 × 10 -01 | 1.49 [0.80-3.61] | 1.08 × 10 -01 | 1.38 [0.93-2.35] | 6.73 × 10 -02 |
tSmiRNA | 8.46 [0.44-164.37] | 5.83 × 10 -02 | 7.13 [1.33-Infinity] | 9.95 × 10 -03 | 0.00 [0.00-Infinity] | <5.00 × 10 -05 |
eQTLs | 4.42 [3.52-5.54] | 7.12 × 10 -45 | 4.67 [3.35-6.39] | <5.00 × 10 -05 | 1.94 [1.61-2.40] | <5.00 × 10 -05 |
vega PseudoGenes | 2.07 [1.35-3.19] | 8.09 × 10 -04 | 1.76 [1.11-3.07] | 1.16 × 10 -02 | 1.10 [0.82-1.58] | 2.85 × 10 -01 |
Intergenic SNPs | 0.89 [0.78-1.01] | 7.19 × 10 -02 | 0.83 [0.71-0.98] | 1.11 × 10 -02 | 0.94 [0.86-1.03] | 8.68 × 10 -02 |
| Â | Â | Conserved regions and evolutionary signatures | Â | Â | Â | |
Evofold | 2.14 [0.63-7.20] | 2.59 × 10 -01 | 1.99 [0.89-Infinity] | 7.47 × 10 -02 | 0.79 [0.40-4.00] | 2.60 × 10 -01 |
Pos. Sel. Genes | 1.96 [1.71-2.24] | 2.05 × 10 -23 | 1.88 [1.60-2.23] | <5.00 × 10 -05 | 1.12 [1.03-1.23] | 6.65 × 10 -03 |
Enhancers | 2.01 [0.76-5.32] | 1.60 × 10 -01 | 1.97 [0.92-12.07] | 5.17 × 10 -02 | 1.02 [0.57-2.67] | 4.72 × 10 -01 |
Exapted Repeats | 1.62 [0.57-4.60] | 4.47 × 10 -01 | 1.67 [0.82-9.04] | 1.23 × 10 -01 | 0.88 [0.46-3.00] | 3.25 × 10 -01 |
PREMOD | 1.63 [1.35-1.97] | 4.22 × 10 -07 | 1.64 [1.38-1.97] | <5.00 × 10 -05 | 1.07 [0.94-1.22] | 1.78 × 10 -01 |
tfbsConsSites | 1.74 [1.41-2.14] | 1.64 × 10 -07 | 1.69 [1.41-2.05] | <5.00 × 10 -05 | 1.02 [0.89-1.18] | 4.23 × 10 -01 |
InDels | 1.80 [1.58-2.05] | 3.61 × 10 -19 | 1.85 [1.66-2.08] | <5.00 × 10 -05 | 1.11 [1.02-1.21] | 7.15 × 10 -03 |
MCS17way | 1.75 [1.52-2.03] | 1.61 × 10 -14 | 1.72 [1.51-1.97] | <5.00 × 10 -05 | 1.01 [0.91-1.11] | 4.62 × 10 -01 |
MCS28wayPlacMammal | 1.96 [1.68-2.28] | 6.51 × 10 -18 | 1.92 [1.67-2.22] | <5.00 × 10 -05 | 1.03 [0.93-1.15] | 3.05 × 10 -01 |
MCS28way | 1.93 [1.67-2.24] | 6.32 × 10 -19 | 1.87 [1.65-2.15] | <5.00 × 10 -05 | 1.00 [0.91-1.11] | 4.99 × 10 -01 |
MCS44way | 2.01 [1.74-2.33] | 2.10 × 10 -21 | 1.96 [1.72-2.24] | <5.00 × 10 -05 | 1.02 [0.93-1.13] | 3.33 × 10 -01 |
MCS44wayPlacental | 1.93 [1.66-2.24] | 5.26 × 10 -18 | 1.89 [1.65-2.17] | <5.00 × 10 -05 | 1.01 [0.92-1.13] | 4.10 × 10 -01 |
MCS44wayPrimates | 2.00 [1.72-2.33] | 1.42 × 10 -19 | 1.98 [1.73-2.30] | <5.00 × 10 -05 | 1.00 [0.91-1.12] | 4.69 × 10 -01 |
Sequence annotation negative | 0.84 [0.74-0.95] | 6.34 × 10 -03 | 0.81 [0.71-0.94] | 1.95 × 10 -03 | 0.91 [0.84-0.99] | 1.53 × 10 -02 |
| Â | Â | Chromatin signatures | Â | Â | Â | |
Open Chromatin | 3.65 [3.18-4.18] | 2.73 × 10 -80 | 3.51 [2.84-4.30] | <5.00 × 10 -05 | 1.31 [1.19-1.44] | <5.00 × 10 -05 |
Closed Chromatin | 0.36 [0.31-0.41] | 1.22 × 10 -51 | 0.30 [0.25-0.38] | <5.00 × 10 -05 | 0.77 [0.70-0.84] | <5.00 × 10 -05 |
Active promoter | 3.22 [2.34-4.43] | 2.27 × 10 -14 | 2.76 [1.99-4.03] | <5.00 × 10 -05 | 1.15 [0.92-1.50] | 1.28 × 10 -01 |
Weak promoter | 3.14 [2.31-4.27] | 7.60 × 10 -15 | 2.82 [2.09-3.98] | <5.00 × 10 -05 | 1.21 [0.98-1.58] | 4.64 × 10 -02 |
Inactive/poised promoter | 4.24 [1.84-9.77] | 2.47 × 10 -04 | 3.65 [1.76-14.19] | 9.50 × 10 -04 | 0.68 [0.40-2.00] | 1.35 × 10 -01 |
Strong enhancer (proximal) | 4.18 [3.14-5.56] | 6.58 × 10 -27 | 3.93 [2.88-5.58] | <5.00 × 10 -05 | 1.48 [1.19-1.89] | 1.50 × 10 -04 |
Strong enhancer (distal) | 2.84 [2.13-3.78] | 8.19 × 10 -14 | 2.71 [2.03-3.78] | <5.00 × 10 -05 | 1.29 [1.05-1.66] | 6.35 × 10 -03 |
Weak/poised enhancer (proximal) | 2.61 [2.01-3.40] | 7.69 × 10 -14 | 2.47 [1.92-3.29] | <5.00 × 10 -05 | 1.08 [0.89-1.32] | 2.32 × 10 -01 |
Weak/poised enhancer (distal) | 2.65 [2.18-3.23] | 1.14 × 10 -23 | 2.57 [2.09-3.20] | <5.00 × 10 -05 | 1.22 [1.06-1.42] | 3.25 × 10 -03 |
Insulator | 1.76 [1.28-2.40] | 4.35 × 10 -04 | 1.69 [1.29-2.32] | 1.50 × 10 -04 | 1.06 [0.86-1.36] | 3.05 × 10 -01 |
Transcriptional transition | 3.22 [2.31-4.48] | 2.50 × 10 -13 | 2.88 [2.08-4.24] | <5.00 × 10 -05 | 1.26 [1.00-1.65] | 3.25 × 10 -02 |
Transcriptional elongation | 2.45 [2.01-2.97] | 1.46 × 10 -20 | 2.13 [1.71-2.69] | <5.00 × 10 -05 | 1.14 [1.00-1.31] | 3.25 × 10 -02 |
Weak transcribed | 2.52 [2.16-2.94] | 7.00 × 10 -34 | 2.33 [1.96-2.80] | <5.00 × 10 -05 | 1.18 [1.06-1.33] | 8.50 × 10 -04 |
Polycomb repressed | 2.06 [1.67-2.52] | 2.85 × 10 -12 | 2.14 [1.66-2.78] | <5.00 × 10 -05 | 1.31 [1.13-1.54] | 1.00 × 10 -04 |
Heterochrom; low signal | 0.56 [0.48-0.64] | 2.85 × 10 -15 | 0.54 [0.45-0.64] | <5.00 × 10 -05 | 0.94 [0.85-1.05] | 1.39 × 10 -01 |
Repetitive/CNV (proximal) | 1.85 [0.49-7.04] | 3.36 × 10 -01 | 1.27 [0.54-6.02] | 6.65 × 10 -01 | 0.33 [0.18-1.00] | 1.86 × 10 -02 |
Repetitive/CNV (distal) | 0.32 [0.03-2.98] | 6.25 × 10 -01 | 0.25 [0.11-Infinity] | 3.02 × 10 -02 | 0.63 [0.33-3.00] | 1.46 × 10 -01 |
DNase Clusters | 2.60 [2.28-2.96] | 7.63 × 10 -48 | 2.64 [2.36-2.97] | <5.00 × 10 -05 | 1.15 [1.06-1.26] | 3.00 × 10 -04 |
Human Insulators | 2.14 [1.63-2.82] | 2.19 × 10 -08 | 1.94 [1.50-2.61] | <5.00 × 10 -05 | 0.99 [0.83-1.23] | 4.61 × 10 -01 |