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Table 2 Conservation and relative single nucleotide polymorphism (SNP) density in different types of functional regions.

From: Functional single nucleotide polymorphism-based association studies

  Odds ratio ± standard error Fold conservation
Transcriptsa 0.895 ± 0.003 12.0×
Transcripts: coding regions 0.762 ± 0.004 16.4×
Transcripts: non-coding 1.072 ± 0.004 6.2×
Conserved elementsb 0.748 ± 0.002 23.5×
Promoterc 0.995 ± 0.005 3.5×
Splice junctionsd 0.780 ± 0.007 10.3×
  1. For each functional region, we report the odds ratio that a nucleotide in that region will be a variant by comparison with the rest of the genome (essentially, the relative SNP density) and standard error. The expected number is obtained using the validated SNP in the genome (4.9 M) and the total number of base pairs of the genome within a particular class of functional elements. A number less than 1 indicates a deficiency in SNP number. We also report the fold conservation (as defined previously [112]) compared with the genome average.
  2. 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/.
  3. b Defined previously [112] and obtained from the University of California, Santa Cruz website http://genome.ucsc.edu/.
  4. c Within 500 base pairs (bp) upstream of the transcription start site.
  5. d Within 20 bp of splice junctions.