Answers.Body: <p>Here is one definition of the classical MHC region: <a href="https://www.ncbi.nlm.nih.gov/grc/human/regions/MHC?asm=GRCh38.p13" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/grc/human/regions/MHC?asm=GRCh38.p13</a></p>
  <p>which defines it as the 5mb region chr6:28510120-33480577 in GRCh38 coordinates.</p>
  <p>The &quot;extended MHC&quot; defined here [1] is 7.2 mb and encompasses an additional &quot;extended Class I&quot; region upstream of the region given above. The xMHC is defined in [1] as the regions between <em>HIST1H2AA</em> and <em>RPL12P1</em> genes, which would give you chr6:25726063-33400644 in Grch38. This is very similar to your HIST1H2AA - KIFC1 definition (chr6:25726063-33410226). Of course if you're trying to reproduce a result, probably better to use the original paper's definition.</p>
  <p>[1] <a href="https://www.nature.com/articles/nrg1489" rel="nofollow noreferrer">https://www.nature.com/articles/nrg1489</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-02T21:56:58.637Z
Answers.Text: Thanks! Sounds like the 2004 _Nat Rev Genetics_ article titled [Gene map of the extended human MHC](https://www.genenames.org/files/PMID15573121.pdf) that you link to is the most authoritative source for the xMHC boundaries. I see in Figure 1, the xMHC goes from HIST1H2AA (extended class I subregion) to RPL12P1 (extended class II subregion). The flanking regions in grey are not part of the xMHC.
  
  Note that RPL12P1 is contained within KIFC1, such that KIFC1 starts before and ends after RPL12P1 in coordinate space.
Answers.UserDisplayName: Daniel Himmelstein
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-02T22:56:46.877Z
Answers.Text: Here is a [MyGene.info query](https://mygene.info/v3/query?q=hg38.chr6:25,726,063-33,410,226&fields=entrezgene,symbol,type_of_gene&species=human&size=1000&entrezonly=true) that returns all NCBI gene IDs and symbols in between `chr6:25,726,063-33,410,226` for GRCh38. I like these boundaries since KIFC1 extends past RPL12P1. For some reason RPL12P1 is not included in the MyGene results. Not sure why. It is a pseudogene, but other pseudogenes are included. The MyGene query currently returns 318 genes.
Answers.UserDisplayName: Daniel Himmelstein
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-02T23:18:01.223Z
Answers.Text: The approved symbol for  `ncbigene:221613` is now H2AC1 rather than HIST1H2AA. KIFC1 is `ncbigene:3833`. RPL12P1 is `ncbigene:729727`.
Answers.UserDisplayName: Daniel Himmelstein
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-02T14:01:08.067Z
Answers.LastActivityDate: 2020-11-02T14:30:31.163Z
Answers.LastEditDate: 2020-11-02T14:30:31.163Z
Answers.UserDisplayName: timodonnell
Body: <p>Is there an accepted boundary of the <em>extended</em> major histocompatibility complex (xMHC) in human? Specifically, I am interested in the boundary coordinates for Genome Reference Consortium Human Build 38 (GRCh38 / hg38).</p>
  <p>I'd like to use these coordinates to query MyGene.info to retrieve a list of genes in the xMHC. For example, King et al 2019 <a href="https://doi.org/10.1371/journal.pgen.1008489.s002" rel="nofollow noreferrer" title="S2 Data. Updating Pipeline Data: Supplementary Methods And Results">used</a> the following definition:</p>
  <blockquote>
  <p>we excluded drugs with nonhuman or xMHC gene targets. We considered xMHC to include HIST1H2AA and KIFC1 and all genes between them (Chromosome 6 25.7 Mb-33.4 Mb).</p>
  </blockquote>
  <p>But I was curious whether there was an authoritative definition of the xMHC region in humans that would specify down the the base pair rather than just megabase pair.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-29T01:53:18.357Z
Comments.Text: This is an extremely good question, these genomic coordinates of course exist, the only thing is MHC ... would include mice as well as humans.  The HLA.is very well defined but  I think you need to ask an immunologist because it is common knowledge, but I don't think any one here knows.
Comments.UserDisplayName: M__
Tags: <gene><genomics><human-genome><human>
Title: What are the coordinates of the extended major histocompatibility complex (xMHC) in GRCh38?
ThreadText: # What are the coordinates of the extended major histocompatibility complex (xMHC) in GRCh38?
  
  (Asked by: username_0 on 2020-10-26)
  
  Is there an accepted boundary of the *extended* major histocompatibility complex (xMHC) in human? Specifically, I am interested in the boundary coordinates for Genome Reference Consortium Human Build 38 (GRCh38 / hg38).
  
  I'd like to use these coordinates to query MyGene.info to retrieve a list of genes in the xMHC. For example, King et al 2019 [used](https://doi.org/10.1371/journal.pgen.1008489.s002 "S2 Data. Updating Pipeline Data: Supplementary Methods And Results") the following definition:
  
  > we excluded drugs with nonhuman or xMHC gene targets. We considered xMHC to include HIST1H2AA and KIFC1 and all genes between them (Chromosome 6 25.7 Mb-33.4 Mb).
  
  But I was curious whether there was an authoritative definition of the xMHC region in humans that would specify down the the base pair rather than just megabase pair.
  
  **Tags:** gene, genomics, human-genome, human
  
  > **Comments:**
  > **username_1**: This is an extremely good question, these genomic coordinates of course exist, the only thing is MHC ... would include mice as well as humans.  The HLA.is very well defined but  I think you need to ask an immunologist because it is common knowledge, but I don't think any one here knows.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-11-02. Score: 4
  
  Here is one definition of the classical MHC region: <https://www.ncbi.nlm.nih.gov/grc/human/regions/MHC?asm=GRCh38.p13>
  
  which defines it as the 5mb region chr6:28510120-33480577 in GRCh38 coordinates.
  
  The "extended MHC" defined here [1] is 7.2 mb and encompasses an additional "extended Class I" region upstream of the region given above. The xMHC is defined in [1] as the regions between *HIST1H2AA* and *RPL12P1* genes, which would give you chr6:25726063-33400644 in Grch38. This is very similar to your HIST1H2AA - KIFC1 definition (chr6:25726063-33410226). Of course if you're trying to reproduce a result, probably better to use the original paper's definition.
  
  [1] <https://www.nature.com/articles/nrg1489>
  
  > **Comments:**
  > **username_0**: Thanks! Sounds like the 2004 _Nat Rev Genetics_ article titled [Gene map of the extended human MHC](https://www.genenames.org/files/PMID15573121.pdf) that you link to is the most authoritative source for the xMHC boundaries. I see in Figure 1, the xMHC goes from HIST1H2AA (extended class I subregion) to RPL12P1 (extended class II subregion). The flanking regions in grey are not part of the xMHC.  Note that RPL12P1 is contained within KIFC1, such that KIFC1 starts before and ends after RPL12P1 in coordinate space.  
  > **username_0**: Here is a [MyGene.info query](https://mygene.info/v3/query?q=hg38.chr6:25,726,063-33,410,226&fields=entrezgene,symbol,type_of_gene&species=human&size=1000&entrezonly=true) that returns all NCBI gene IDs and symbols in between `chr6:25,726,063-33,410,226` for GRCh38. I like these boundaries since KIFC1 extends past RPL12P1. For some reason RPL12P1 is not included in the MyGene results. Not sure why. It is a pseudogene, but other pseudogenes are included. The MyGene query currently returns 318 genes.  
  > **username_0**: The approved symbol for  `ncbigene:221613` is now H2AC1 rather than HIST1H2AA. KIFC1 is `ncbigene:3833`. RPL12P1 is `ncbigene:729727`.  
  
  ---
  
  