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LOC121366033 H3K4me1 hESC enhancer GRCh37_chr9:136322178-136323045 [ Homo sapiens (human) ]

Gene ID: 121366033, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121366033
Gene description
H3K4me1 hESC enhancer GRCh37_chr9:136322178-136323045
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive and primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (133457056..133457923)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (145671490..145672357)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (136322569..136322863)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136234564-136235235 Neighboring gene surfeit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20456 Neighboring gene serine/threonine kinase like domain containing 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:136257045-136257682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136265498-136266135 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136267839-136268006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136269742-136270242 Neighboring gene REX4 homolog, 3'-5' exonuclease Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29238 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20458 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136295843-136296052 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136321575-136321727 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136327558-136328114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29242 Neighboring gene uncharacterized LOC124902295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20462 Neighboring gene calcium channel flower domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136344231-136344732 Neighboring gene solute carrier family 2 member 6

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 9315

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_074383.2 

    Range
    101..968
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    133457056..133457923
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646201.1 Reference GRCh38.p14 PATCHES

    Range
    283150..284017
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    145671490..145672357
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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