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Table 3 SNP density per kilobase (kb) and counts in different types of functional regions.

From: Functional single nucleotide polymorphism-based association studies

  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)
  1. 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).
  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.
  6. e SNPs per kb ± standard error of the mean (total number of SNPs).