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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).
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Human Genomics

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