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. 2022 Dec 22;51(3):e18. doi: 10.1093/nar/gkac1198

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© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 3. — Comparison of snpSTARRseq to orthogonal methodologies. (A) snpSTARRseq allelic-effects (ALT/REF; Method; Log₂FoldChange) was compared to DeltaSVM (Essentiality Score), ncER (Essentiality Score) and CADD (PHRED score) and no significant relation found. (B) snpSTARRseq allele frequency (AF) values were compared against in-vivo AF obtained by H3k27Ac and AR ChIPseq and ATACseq. The top row contains all SNP values without any filtration whereas the bottom row has only significant SNPs found by snpSTARRSeq (nominal p-value < 0.05). Two anecdotal examples of repressive (purple) and activating (blue) SNPs were colored to which were found by all 4 methodologies. (C) SNPs with activating and repressive effects found by previous in vivo work and snpSTARRseq were demonstrated. snpSTARRseq captures the bi-allelic effect of these SNPs accurately.