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.