Table 3.
SNP density per kilobase (kb) and counts in different types of functional regions.
| Transcriptsa | Coding regions | Conserved elementsb | Promoterc | Splice junctiond | |
|---|---|---|---|---|---|
| Transcripts | 1.46 ± 0.005e (87065) | ||||
| Coding regions | 1.24 ± 0.006 (42387) | 1.24 ± 0.006 (42387) | |||
| Conserved elements | 1.03 ± 0.006 (31339) | 0.98 ± 0.006 (23397) | 1.22 ± 0.003 (170256) | ||
| Promoter | 1.65 ± 0.038 (1854) | 1.38 ± 0.06 (533) | 1.03 ± 0.02 (2732) | 1.62 ± 0.01 (28463) | |
| Splice junctions | 1.11 ± 0.012 (8728) | 1.06 ± 0.012 (7519) | 1.07 ± 0.013 (7149) | 1.46 ± 0.086 (292) | 1.27 ± 0.009 (19225) |
The diagonal provides single nucleotide polymorphism (SNP) density for each region type and the off-diagonal provides density for regions of two types, either because one type is a subtype (coding is a subtype of transcript) or because of overlapping transcript definitions (a region may be in the promoter of one transcript, yet coding in another).
a Includes coding regions and untranslated regions (including RNA genes). All SNPs and the definitions of gene elements were obtained from the Ensembl database http://www.ensembl.org/.
b Defined previously [112] and obtained from the University of California, Santa Cruz website http://genome.ucsc.edu/.
c Within 500 base pairs (bp) upstream of the transcription start site.
d Within 20 bp of splice junctions.
e SNPs per kb ± standard error of the mean (total number of SNPs).