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mecfs_bio.constants.genomic_coordinate_constants

Note: According to the paper Horton, Roger, et al. "Gene map of the extended human MHC." Nature Reviews Genetics 5.12 (2004): 889-899. The extended MHC region is defined as being between the HIST1H2AA gene and the RPL12P1 pseudo-gene.

According to https://www.genecards.org/cgi-bin/carddisp.pl?gene=H2AC1,
HIST1H2AA starts at position 25726291 in genome build 37

According to https://www.genecards.org/cgi-bin/carddisp.pl?gene=RPL12P1

RPL12P1 ends at genome position 33368421 in genome build 37

The build-38 bounds use the same two boundary genes in GRCh38 (GeneCards):
H2AC1 (HIST1H2AA) spans chr6:25723397-25726562 and RPL12P1 spans
chr6:33400015-33400644, so the extended MHC brackets [25723397, 33400644].
Excluding this region is standard for LD-score regression (its long-range,
atypical LD violates the LD-score model; cf. Bulik-Sullivan et al. 2015).

Functions:

Attributes:

EXTENDED_MHC_BUILD_37 module-attribute 

EXTENDED_MHC_BUILD_37 = GenomicInterval(
    start=EXTENDED_MHC_START_BUILD_37,
    end=EXTENDED_MHC_END_BUILD_37,
    chrom=6,
)

EXTENDED_MHC_BUILD_38 module-attribute 

EXTENDED_MHC_BUILD_38 = GenomicInterval(
    start=EXTENDED_MHC_START_BUILD_38,
    end=EXTENDED_MHC_END_BUILD_38,
    chrom=6,
)

EXTENDED_MHC_END_BUILD_37 module-attribute 

EXTENDED_MHC_END_BUILD_37 = 33368421

EXTENDED_MHC_END_BUILD_38 module-attribute 

EXTENDED_MHC_END_BUILD_38 = 33400644

EXTENDED_MHC_START_BUILD_37 module-attribute 

EXTENDED_MHC_START_BUILD_37 = 25726291

EXTENDED_MHC_START_BUILD_38 module-attribute 

EXTENDED_MHC_START_BUILD_38 = 25723397

GenomeBuild module-attribute 

GenomeBuild = Literal['19', '38']

MHCRegion module-attribute 

MHCRegion = Literal['classical', 'extended']

extended_mhc_interval 

extended_mhc_interval(
    build: GenomeBuild,
) -> GenomicInterval

Return the extended MHC region for the given genome build (19/GRCh37 or 38/GRCh38), bracketed by the HIST1H2AA and RPL12P1 boundary genes.

Source code in mecfs_bio/constants/genomic_coordinate_constants.py 
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def extended_mhc_interval(build: GenomeBuild) -> GenomicInterval:
    """Return the extended MHC region for the given genome build (19/GRCh37 or
    38/GRCh38), bracketed by the HIST1H2AA and RPL12P1 boundary genes."""
    if build == "19":
        return EXTENDED_MHC_BUILD_37
    if build == "38":
        return EXTENDED_MHC_BUILD_38
    raise ValueError(f"Extended MHC region not implemented for genome build {build}")