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. Author manuscript; available in PMC: 2020 Jul 7.
Published in final edited form as: Nat Genet. 2020 Jan 7;52(1):56–73. doi: 10.1038/s41588-019-0537-1

Figure 3. Overlap of CCVs with gene regulatory regions gene bodies and transcription factor binding sites.

Figure 3

(a) Breast cancer CCVs overlap with chromatin states and broad breast cells epigenetic marks. (b) Breast cancer CCVs overlap with breast cells epigenetic marks. (c) Autoimmune CCVs overlap with breast cells epigenetic marks. (d) Breast cancer CCVs overlap with autoimmune-related epigenetic marks. (e) Autoimmune CCVs overlap with autoimmune-related epigenetic marks. (f) Significant ER-positive CCVs overlap with transcription factors binding sites. TFBSs found significant for ER-positive CCVs are highlighted in red (x axis labels). (g) Significant ER-negative CCVs overlap with transcription factors binding sites. (h) Significant ER-neutral CCVs overlap with transcription factors binding sites. Strong column: analysis with all CCVs at strong signals. ER-positive, ER-negative, ER-neutral: analysis of CCVs at strong signals stratified by phenotype. Logistic regression robust variance estimation for clustered observations, Wald test Χ2 p-values estimated using 67,136 ER-positive and 17,506 ER-negative cases, together with 88,937 controls.

Non-significant p-values are noted as dark grey. Significance defined as FDR 5%, which corresponds to the following P-value thresholds: Strong signals P-value = 1.66x10-2, ER-positive P-value = 2.42x10-2; ER-negative P-value 3.02x10-3; ER-neutral P-value = 1.76x10-3.