How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features from UCSC genome browser (e.g. number of CpG islands per gene, number of DNase clusters per gene, regulatory enrichment scores etc.) however I am not sure how to control for bias where a gene that is larger in length – and so will then have more CpG islands or higher regulatory enrichment scores simply due to gene length.

Is there a way to correct for gene length when taking/condensing variant data to individual genes?

Edit:

For reference, my machine learning model aims to predict whether a gene is the most likely to be causal for a disease (out of all the genes given to the model). The model will score the genes as a regression classification between 0 to 1 (0 being least likely to cause disease and 1 being most likely to cause disease). I plan to later further investigate the genes with the highest scores.

The model uses a variety of multi-omic features (e.g. GTEx gene expression the genes have for many tissues, GWAScatalog data, gene intolerance scores, protein-protein interaction data, drug interaction data, phenotypic scores etc.). However, I am missing epigenetic data to describe my genes so I’ve been looking to collect based on UCSC’s variant data (CpG islands, histone modifications, DNase clusters) – however this leads to my gene length problem when I am trying to reliably take data from the variant level.

I’ve been plotting my features and gene length, and seen that the UCSC epigenetic data does correlate with having a larger gene length if there is a higher count of regulatory sites (0.8 r2 for some), and so this is what I’m looking to correct.