Table 2.
Overview of Genomic Analyses and Results
| Feature | rQTL | intQTL |
|---|---|---|
| Median length (range) | 2.52 (0.11–11.5) Mbp | 1.79 (0.42–12.7) Mbp |
| GC content (range) | 0.41 (0.37–0.52) | 0.42 (0.37–0.48) |
| Interval composition | ||
| Intergenic | 67.7% | 60.1% |
| UTR | 1.4% | 1.9% |
| Coding exon | 1.1% | 1.2% |
| Intron | 29.8% | 37.1% |
| SNP density (median) | ||
| nsyn SNP/N | 5.53 E−4 (0–0.01) | 5.96 E−4 (0–0.02) |
| syn SNP/S | 4.54 E−3 (0–0.05) | 4.42 E−3 (0–0.04) |
| SNP/intron | 2.94 E−1 | 1.14 E−3 |
| SNP/3′-UTR | 6.50 E−3 | 6.74 E−4 |
| SNP/5′-UTR | 2.95 E−3 | 6.84 E−2 |
| SNP/TFBS | 1.46 E−3 | 1.20 E−3 |
| Correlation of sequence-type SNP densities | High correlation of SNP densities between all parts of the sequence, except with introns | High correlation of SNP densities between all parts of the sequence, except with exons |
| Overlap with genes differentially expressed in limbs (Cotney et al. 2012) | 22 genes (P = 6.2 E−5) | 30 genes (P = 2.1 E−7) |
| Overlap with limb-specific enhancers (Cotney et al. 2012) | Total enhancers: 535; polymorphic: 224 (high overlap); polymorphic enhancers present in 70% rQTL | Total enhancers: 1,100; polymorphic: 140; polymorphic enhancers present in 12% intQTL |
| Overlap with limb-type -specific enhancers (Cotney et al. 2012) | Total enhancers: 39; polymorphic: 7; polymorphic enhancers present in 15% rQTL | Total enhancers: 69; polymorphic: 8; polymorphic enhancers present in 8% intQTL |