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LOC112577554 H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:230468147-230468791 and GRCh37_chr1:230468792-230469436 [ Homo sapiens (human) ]

Gene ID: 112577554, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577554
Gene description
H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:230468147-230468791 and GRCh37_chr1:230468792-230469436
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. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. An overlapping subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 22:ReprW, weaker Polycomb repression) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC112577554 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (230332401..230333690)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (229712872..229714161)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (230468509..230468803)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene polypeptide N-acetylgalactosaminyltransferase 2 Neighboring gene uncharacterized LOC124904542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230400862-230401362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230401363-230401863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230402952-230403462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230403463-230403971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230403972-230404481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230404482-230404990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230422195-230422694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230423879-230424378 Neighboring gene NANOG hESC enhancer GRCh37_chr1:230431082-230431583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1939 Neighboring gene putative uncharacterized protein FLJ46204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230452427-230452928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230452929-230453428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2718 Neighboring gene piggyBac transposable element derived 5 Neighboring gene uncharacterized LOC124904543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230535746-230536379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230562153-230562700 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:230562701-230563247 Neighboring gene uncharacterized LOC105373164

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230468147-230468791
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230468792-230469436
  • Sharpr-MPRA regulatory region 8330

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_060471.2 

    Range
    101..1390
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    230332401..230333690
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    229712872..229714161
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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