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LOC127815261 H3K4me1 hESC enhancer GRCh37_chr9:95951526-95952459 [ Homo sapiens (human) ]

Gene ID: 127815261, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127815261
Gene description
H3K4me1 hESC enhancer GRCh37_chr9:95951526-95952459
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. A subregion containing a Neanderthal adaptively introgressed expression-modulating variant (emVar) was additionally validated as a functional enhancer by MPRAs in K562 erythroleukemia cells, with activity observed for the non-introgressed 9:95951769 or rs7041800 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC127815261 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (93189244..93190177)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (105355859..105356792)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (95951526..95952459)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95897247-95897843 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95905234-95906106 Neighboring gene ninjurin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95906107-95906979 Neighboring gene Sharpr-MPRA regulatory region 13679 Neighboring gene uncharacterized LOC124902213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95913665-95914165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95935533-95936106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95948459-95949424 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:95955296-95955514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95964080-95965013 Neighboring gene WNK lysine deficient protein kinase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96000334-96000834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96007029-96007528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96025151-96025819 Neighboring gene uncharacterized LOC124902214 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96050932-96051728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96061034-96061534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96063483-96064395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96068651-96069555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96088631-96089132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96089133-96089632 Neighboring gene family with sequence similarity 120A2, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, Free PMC Article
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Neanderthal introgressed variant-containing enhancer experimental_109868
  • emVar-containing allelic enhancer experimental_109868

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_116777.1 

    Range
    101..1034
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    93189244..93190177
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    105355859..105356792
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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