To evaluate the enrichment of all nominal significant nsCL/P GWAS SNPs (74) in a priori selected regulatory elements, the GREGOR (v1.4.0) (62) software tool was used. Selection of the regions was performed on the basis of the presence of p63 and/or KLF4 and/or H3K27ac peaks. For analysis of overlay of specific SNPs to specific elements, a colocalization approach was performed as previously suggested (14). Briefly, SNPs were mapped to either “positive regions” (i.e., in p63 + KLF4 ± H3K27ac binding regions) or “negative regions” (all others) and then grouped into nine categories 10k+1P > 10k for k = 1,…, 8 and 10−8P. The frequencies of SNPs located in the positive regions and those outside the annotated regions were counted within each category. The one-sided Cochran-Armitage trend test was applied in R environment with function prop.trend.test of stats package to test for an enrichment of smaller P values within annotated regions based on the resulting 9 × 2 contingency table.

Note: The content above has been extracted from a research article, so it may not display correctly.

Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.

We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.