Table 1

Odds ratios of sampling and permutations for two datasets
Sampling Permutations
Significantly associated SNPs Significantly associated SNPs Suggestively associated SNPs
OR [95% CI] P-value OR [95% CI] P-value OR [95% CI] P-value
Genic and regulatory features
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
Conserved regions and evolutionary signatures
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
Chromatin signatures
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

Kindt et al.

Kindt et al. BMC Genomics 2013 14:108   doi:10.1186/1471-2164-14-108

Open Data