Sequence features in regions of weak and strong linkage disequilibrium

Table 1.

Spearman rank correlation between disequilibrium and sequence features in windows of 100, 500, and 1000 kb
CEU sample
YRI sample
CHB+JPT sample
100 kb
 500 kb
 1000 kb
 100 kb
 500 kb
 1000 kb
 100 kb
 500 kb
 1000 kb
LD in other populations
    CEU 1.00* 1.00* 1.00* 0.81* 0.86* 0.89* 0.86* 0.89* 0.90*
    YRI 0.81* 0.86* 0.88* 1.00* 1.00* 1.00* 0.80* 0.85* 0.88*
    CHB+JPT 0.84* 0.88* 0.89* 0.79* 0.84* 0.87* 1.00* 1.00* 1.00*
Basic sequence features
    GC content -0.33* -0.33* -0.33* -0.34* -0.34* -0.35* -0.33* -0.33* -0.33*
    CpG Islands -0.07* -0.13* -0.17* -0.06* -0.13* -0.18* -0.07* -0.12* -0.16*
    Polymorphism (π) -0.38* -0.43* -0.42* -0.37* -0.40* -0.39* -0.36* -0.41* -0.41*
Genes and related features
    Gene count 0.01 -0.04* -0.08* 0.01 -0.05* -0.08* 0.01 -0.04* -0.07*
    Genic bases (intron, exon, UTR) 0.05* 0.00 -0.03 0.05* -0.01 -0.05* 0.05* 0.00 -0.03
    Coding bases 0.03* -0.02 -0.06* 0.03* -0.02 -0.06* 0.03* -0.02 -0.05
    Exonic bases 0.01 -0.04* -0.08* 0.01 -0.04* -0.09* 0.01 -0.04 -0.07*
    Intronic bases 0.05* 0.00 -0.03 0.04* -0.01 -0.05* 0.05* 0.00 -0.03
    UTR (3′ and 5′) -0.01 -0.06* -0.10* -0.01 -0.06* -0.11* -0.01 -0.06* -0.09*
Other features
    Bases in transcription factor binding sites -0.10* -0.10* -0.09* -0.11* -0.11* -0.10* -0.10* -0.10* -0.09*
    Bases in transcribed fragmentsa -0.03* -0.03 -0.03 -0.03* -0.02 -0.02 -0.03* -0.02 -0.02
    Predictions of conserved elements (phastCons) -0.09* -0.08* -0.07* -0.09* -0.09* -0.09* -0.09* -0.08* -0.07*
    Identical base in alignment with M. musculus -0.19* -0.19* -0.17* -0.20* -0.20* -0.19* -0.19* -0.19* -0.17*
    Conserved noncoding sequence -0.16* -0.14* -0.12* -0.17* -0.15* -0.13* -0.16* -0.14* -0.12*
    Identical base in alignment with R. norvegicus -0.18* -0.18* -0.17* -0.19* -0.20* -0.18* -0.18* -0.19* -0.17*
Repeat content
    Total bases in repeats 0.25* 0.34* 0.35* 0.26* 0.36* 0.37* 0.25* 0.33* 0.34*
    Bases in LINE repeats 0.27* 0.34* 0.36* 0.27* 0.34* 0.37* 0.27* 0.33* 0.36*
    Bases in SINE repeats -0.12* -0.15* -0.18* -0.11* -0.15* -0.19* -0.12* -0.14* -0.17*
    Bases in LTR repeats 0.00 0.06* 0.09* -0.01 0.08* 0.11* 0.00 0.06* 0.08*
    Bases in DNA repeats -0.03* -0.08* -0.12* -0.03* -0.09* -0.13* -0.03* -0.08* -0.11*
    Bases in simple repeats -0.21* -0.28* -0.31* -0.21* -0.26* -0.29* -0.20* -0.27* -0.30*
    Bases in low complexity repeats 0.04* 0.04* 0.03 0.05* 0.07* 0.06* 0.05* 0.06* 0.04
    Bases in satellite repeats 0.03* 0.02 0.04 0.02* 0.02 0.04 0.02* 0.03 0.04
    Bases in other repeats
0.05*
0.07*
0.08*
0.06*
0.08*
0.08*
0.05*
0.08*
0.09*

  • ↵* Correlation is significant at P < 0.0001 level.

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

This Article

  1. Genome Res. 15: 1519-1534

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