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Something I've never been quite clear on is the difference between in cis/in trans and in phase/out of phase (in the context of diploid organisms).

My understanding is that the in cis/in trans terminology is used specifically when referring to the configuration of recessive and dominant alleles for a pair of genes, while in phase/out of phase is used when referring to a pair of individual variants, such as SNPs or indels, however it would be great to get an authoritative clarification on the issue.

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    $\begingroup$ Like all words, the meaning of terms like these strongly depends on context — quotes (with appropriate citations) would probably be your best bet for getting a clear answer, but at very least you need to provide more information than "in diploid organisms". $\endgroup$
    – tyersome
    Apr 26 at 1:22
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    $\begingroup$ Posts must be self-contained — if I need to search on youtube to understand your question it is not finished! 2) You are expected to demonstrate that you have done the expected prior research — that means consulting textbooks and other reliable sources before posting. Youtube videos are of highly variable quality and I don't have time to vet them. Please edit your question and tell us where you've looked for answers (not "youtube"), what you do know about the topic, and where exactly you still have questions. Please take the tour and consult the help center starting with How to Ask for details. $\endgroup$
    – tyersome
    Apr 26 at 4:54

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Unless there are other meanings of the terms I'm not aware of, they are referring to slightly different things.

Haplotype 'phase' refers to whether alleles are found on the same chromosome (paternal or maternal). Hence, 'phasing' refers to the statistical / read-based process of determining which chromosome a genetic variant is found on. 'Unphased' data, typically produced by genotyping arrays or sequencing technology (e.g. short Illumina reads), doesn't contain information about which chromosome a variant is on.

In some contexts, cis/trans terminology refers to whether a locus (e.g. a eQTL/pQTL) is found near the gene it corresponds to. For instance, say you run a GWAS on protein levels and find a significant hit for a locus controlling the level of the protein X. If this locus is within some kind of threshold distance of the gene encoding protein X, perhaps 2Mb, then it is known as a 'cis' ('on the same side as'). Otherwise, if the locus is found distal to gene encoding protein X, it is known as a 'trans' locus. Similarly, 'cis' regulatory elements are regions of non-coding DNA which regulate the transcription of nearby genes.

For example, from this paper:

In the cis-eQTL analysis, we evaluated the associations between lncRNA expression levels and the genotype at a given SNP locus located within 1 Mb upstream and 1 Mb downstream of lncRNA. trans-eQTLs are defined as associations beyond the 2-Mbp interval.

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  • $\begingroup$ I took a closer look a number of Wikipedia articles, including those you linked to. The Latin root of cis/trans means this side of/the other side of, which calls to mind pairs of chromosomal homologs, however modern usage of the terminology appears to mean something more like same molecule/different molecule. Whether or not acting "in cis" requires that the action is in some way facilitated by the genetic elements all belonging to the same DNA molecule is left unclear, and "in trans" is still sometimes used for distant but still chromosomally co-located genetic elements. $\endgroup$
    – Thoth
    Apr 25 at 21:03
  • $\begingroup$ Can you provide a citation for the use of cis/trans that you give — you seem to be saying it is primarily about proximity, which conflicts with the usages I've encountered in biology (and chemistry) ... $\endgroup$
    – tyersome
    Apr 26 at 1:34
  • $\begingroup$ @tyersome could you be more specific about what use I refer to that you're interested in more information about? If you mean the use stated in my original post, then just go on YouTube and type in "cis trans genes", the top hits will all be videos explicating the so called cis/trans configurations of recessive and dominant alleles. $\endgroup$
    – Thoth
    Apr 26 at 3:46
  • $\begingroup$ @Thoth given there seems to be different definitions of cis/trans, you should really give the context with which you are asking this question. $\endgroup$
    – user438383
    Apr 26 at 11:19
  • $\begingroup$ @user438383 in the context of genomics/genetics. $\endgroup$
    – Thoth
    Apr 26 at 17:05

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