This page presents an online browser of multi-layer noncoding variant prioritization results based on a multi-ancestry GWAS of blood lipids involving 1.6 million individuals from five ancestries (Graham et al, Nature, 2021).
The multi-layer noncoding variant prioritization methods and results are described in the following article:
Ramdas et al. A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids. bioRxiv (2021). https://doi.org/10.1101/2021.12.07.470215
If you find the multi-layer noncoding variant prioritization methods and results useful for your work, please kindly cite the research article listed above (Ramdas et al, bioRxiv, 2021). Correspondence should be addressed to Xiang Zhu (xiangzhu[at]psu[dot]edu) and Christopher D Brown (chrbro[at]upenn[dot]edu).
Here we provide a simple example to showcase the usage of the online data browser. After typing this gene name in the search box below, we only see one functional variant prioritized for RRBP1, which is the same as the index variant (Index==chr20_17844684, hg19). The prioritized variant chr20_17844684 is an eQTL variant for RRBP1 in GTEx liver samples (Tissue == Liver). This variant resides in chromatin regions that are open in both liver and adipose samples (ATAC-seq == Both). This variant has physical interaction with RRBP1 according to Capture-C data from adipose samples (Capture-C == Adipose). This variant resides in Roadmap enhancer regions derived from both liver and adipose samples (Enhancer == Both), and it is not overlapped with Roadmap promoter regions from liver or adipose (Promoter == Blank). The RegulomeDB score of this variant is 0.60906. This variant is also a putative binding site for many transcription factors, as shown in the last column Transcription Factor Binding.
Below is the browser of our full results. The Index column represents the lead/sentinel/index variant (hg19) at a GWAS credible set. The Variant column represents the prioritized noncoding variant (hg19) in the credible set. Note that one GWAS credible set (Index) can have multiple functional variants (Variant). The following columns represent overlap of the functional variant with open chromatin (ATAC-seq), physical interactions with an GTEx eQTL gene (Capture-C), Roadmap enhancer and promoter marks in liver, adipose, both or none of the two tissues, the RegulomeDB score of the prioritized variant, and transcription factors to which the prioritized variant is predicted to be bound.