Table 6.

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

	CEU sample			YRI 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 fragments^a	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.

Sequence features in regions of weak and strong linkage disequilibrium