Table 6.

Sequence composition in hotspots for the rapid breakdown of linkage disequilibrium and other intervals

CEU sample
YRI sample
CHB+JPT sample
Hotspots
Other intervals
Hotspots
Other intervals
Hotspots
Other intervals
Number of intervals 14,525 702,099 15,623 750,857 12,607 610,826
Basic sequence features
    GC content 4379 4056** 4404 4052** 4395 4067**
    CpG islands 72 58 68 56 78 60*
    Polymorphism (π) 13.49 12.33** 13.68 12.15** 13.85 12.49**
Genes and related features
    Genic bases (exon, intron, UTR) 3608 3862** 3543 3835** 3787 3916
    Coding bases 135 131 126 128 143 141
    Exonic bases 273 248 255 240 295 261
    Intronic bases 3385 3663** 3341 3643** 3556 3707*
    UTR (3′ and 5′) 138 117 129 112 152 120*
Other features
    Bases in transcription factor binding sites 124 114** 122 113* 128 115**
    Bases in transcribed fragmentsa 292 280 296 269 290 289
    Predictions of conserved elements (phastCons) 579 532** 560 528* 594 537**
    Identical base in alignment with M. musculus 3112 2889** 3141 2908** 3050 2874**
    Identical base in alignment with R. norvegicus 2999 2803** 3036 2823** 2957 2787**
    Conserved noncoding sequence 183 157** 180 157** 193 157**
Repeat content
    Total bases in repeats 3717 4113** 3732 4142** 3667 4086**
    Bases in LINE repeats 1237 1716** 1249 1741** 1224 1703**
    Bases in SINE repeats 1295 1161** 1281 1160** 1277 1155**
    Bases in LTR repeats 741 774 744 783 722 771*
    Bases in DNA repeats 287 303 294 304 289 302
    Bases in simple repeats 93 79** 93 78** 92 80*
    Bases in low complexity repeats 57 56 56 56 56 56
    Bases in satellite repeats 4 14** 7 10 2 12**
    Bases in other repeats
3
7**
5
7
3
7**

a Only applies to chromosomes 6, 7, 13, 14, 18, 19, 20, 21, 22, and X.

* Hotspots and other intervals differ significantly at P < 0.001 level.

** Hotspots and other intervals differ significantly at P < 0.000001 level.

Average sequence composition (per 10,000 bases) is presented for hotspots and control intervals.