Although many non-coding regions have biological function,<ref name="Costa non-coding32">{{cite book |title=Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection |vauthors=Costa F |date=2012 |publisher=[[Caister Academic Press]] |isbn=978-1-904455-94-3 |veditors=Morris KV |chapter=7 Non-coding RNAs, Epigenomics, and Complexity in Human Cells}}{{page needed|date=June 2022}}</ref><ref name="Nessa32">{{cite book |title=Junk DNA: A Journey Through the Dark Matter of the Genome |vauthors=Carey M |date=2015 |publisher=Columbia University Press |isbn=978-0-231-17084-0 |author-link=Nessa Carey}}{{page needed|date=June 2022}}</ref> muchsome ofgenomes thecontain non-codingsequence DNA in most genomesthat does not have biological function and has been described as "Junk DNA". Though exact definitions differ, this refers broadly to "any DNA sequence that does not play a functional role in development, physiology, or some other organism-level capacity."<ref name="PalazzoGregory20142">{{cite journal |vauthors=Palazzo AF, Gregory TR |date=May 2014 |title=The case for junk DNA |journal=PLOS Genetics |volume=10 |issue=5 |pages=e1004351 |doi=10.1371/journal.pgen.1004351 |pmc=4014423 |pmid=24809441}}</ref> The amount of sequence that falls under this term varies widely between organisms.<ref name=":0" /><ref name=":12" /> The term itself has been contentious as different definitions of what constitutes biological function lead to highly different estimates of what proportion of a genome falls into the category.<ref name=":02">{{cite journal |last1=Palazzo |first1=A F |last2=Kejiou |first2=N S |year=2022 |title=Non-Darwinian Molecular Biology |journal=Front. Genet. |volume=13 |pages=831068 |doi=10.3389/fgene.2022.831068 |pmc=8888898 |pmid=35251134 |doi-access=free}}</ref><ref name=":13">{{cite journal |vauthors=Ponting CP, Hardison RC |date=November 2011 |title=What fraction of the human genome is functional? |journal=Genome Research |volume=21 |issue=11 |pages=1769–1776 |doi=10.1101/gr.116814.110 |pmc=3205562 |pmid=21875934}}</ref> In particular, the [[ENCODE]] project in the 2000s demonstrated detectable biochemical activity resulting from most parts of the genome ([[Transcription (biology)|transcription to RNA]], [[Transcription factor-binding site|transcription factor binding]], etc).<ref name="eddy2">{{cite journal |author-link=Sean Eddy |vauthors=Eddy SR |date=November 2012 |title=The C-value paradox, junk DNA and ENCODE |journal=Current Biology |volume=22 |issue=21 |pages=R898–R899 |doi=10.1016/j.cub.2012.10.002 |pmid=23137679 |s2cid=28289437 |doi-access=free}}</ref><ref>{{Cite journal |last=Celniker |first=Susan E. |last2=Dillon |first2=Laura A. L. |last3=Gerstein |first3=Mark B. |last4=Gunsalus |first4=Kristin C. |last5=Henikoff |first5=Steven |last6=Karpen |first6=Gary H. |last7=Kellis |first7=Manolis |last8=Lai |first8=Eric C. |last9=Lieb |first9=Jason D. |last10=MacAlpine |first10=David M. |last11=Micklem |first11=Gos |last12=Piano |first12=Fabio |last13=Snyder |first13=Michael |last14=Stein |first14=Lincoln |last15=White |first15=Kevin P. |date=2009-06 |title=Unlocking the secrets of the genome |url=https://www.nature.com/articles/459927a |journal=Nature |language=en |volume=459 |issue=7249 |pages=927–930 |doi=10.1038/459927a |issn=1476-4687 |pmc=PMC2843545 |pmid=19536255}}</ref> However, whether this biochemical activity is promiscuous activity in a noisy biological system or evolutionarily relevant biological function has been less clear - and consequently, whether that DNA counts as "junk" or not.<ref name=":13" /><ref name="eddy2" /><ref name=":12">{{cite journal |vauthors=Ponting CP, Hardison RC |date=November 2011 |title=What fraction of the human genome is functional? |journal=Genome Research |volume=21 |issue=11 |pages=1769–1776 |doi=10.1101/gr.116814.110 |pmc=3205562 |pmid=21875934}}</ref><ref name=":13" /><ref name="eddy2" />
==Genome-wide association studies (GWAS) and non-coding DNA==
