A map of constrained coding regions (CCRs) in the human genome.

If you use CCRs in any way, please cite the paper:

Havrilla, J.M., Pedersen, B.S., Layer, R.M. & Quinlan, A.R. A map of constrained coding regions in the human genome. Nature Genetics (2018). doi:10.1038/s41588-018-0294-6

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Note that currently, all files use the hg19/GRCh37 human reference.

CCR Bed File | CCR Tabix Index File | CCR BigWig File

X-CCR Bed File | X-CCR Tabix Index File | X-CCR BigWig File

CCR Browser

So the browser is accessible at www.rebrand.ly/ccrregions (the link shown above) or the hard link at https://s3.us-east-2.amazonaws.com/ccrs/ccr.html. You can use either link to get to the browser, and after either link you can submit a locus as a query to the browser at the end of the URL like so:

• www.rebrand.ly/ccrregions#chr20:62,064,356-62,079,335
• or www.rebrand.ly/ccrregions#20:62,064,356-62,079,335
• or www.rebrand.ly/ccrregions#chr20:62064356-62079335
• or www.rebrand.ly/ccrregions#20:62064356-62079335
• or www.rebrand.ly/ccrregions#KCNQ2

Additionally you can do multi-locus search in the URL (or separated by spaces in the search bar of IGV) like so:

• www.rebrand.ly/ccrregions#chr20:62,064,356-62,079,335+ACTN1
• or www.rebrand.ly/ccrregions#KCNQ2+ACTN1
• or www.rebrand.ly/ccrregions#KCNQ2+ACTN1+ACTN2

BED file columns

Column	Description
chrom	Chromosome ID
start	Start coordinate (may be part of a multi-exon CCR)
end	End coordinate (may be part of a multi-exon CCR)
ccr_pct	CCR percentile. 0 represents ExAC variants and is total non-constraint. 100 represents complete constraint, the highest constrained region in the model.
gene	HGNC gene name.
ranges	The range of coordinates that represent the CCR. For multi-exon spanning CCRs, this will be a comma-separated list of ranges.
varflag	VARTRUE = 0th percentile CCR, and thus an ExAC variant coordinate (or several ExAC deletions merged into one CCR). VARFALSE = Anything that is not a 0th percentile CCR.
syn_density	A calculation of the synonymous variant density of the CCR region. Used variants that were SNPs and did not change amino acids or stop/start codons. Allowed multiple alleles at same bp.
cpg	CpG dinucleotide density of the whole CCR region.
cov_score	The score of length scaled by coverage proportion at 10x for each base pair.
resid	Raw residual value from the linear regression model.
resid_pctile	Raw residual percentile, not weighted by proportion of exome represented.
unique_key	A unique key ID for each CCR.