Positional weight matrices have sufficient prediction power for analysis of noncoding variants.

Finally, we tested if the PWM predictions agreed with the allelic binding ratios in HepG2 ChIP-seq data and found a small but marginally significant correlation ( Figure 2f, r = 0.194, P = 0.052) for 101 SNPs tested in Yan et al . and reaching r = 0.235 ( P = 0.047) for a subset of 72 SNPs with significant PWM CIS-BP hits (motif P -value < 0.005), in contrast to almost zero correlation for ΔPWM Mult reported in Yan et al .

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