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LOC115804234 H3K4me1 hESC enhancers GRCh37_chr1:181110258-181110758 and GRCh37_chr1:181110759-181111259 [ Homo sapiens (human) ]

Gene ID: 115804234, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115804234
Gene description
H3K4me1 hESC enhancers GRCh37_chr1:181110258-181110758 and GRCh37_chr1:181110759-181111259
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 represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. Two subregions marked by the H3K4me1 histone modification were shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. A subregion was also validated as a high-confidence cis-regulatory element for the IER5 (immediate early response 5) gene on chromosome 1 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (181141122..181142123)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (180496556..180497557)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (181110563..181111112)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2173 Neighboring gene Sharpr-MPRA regulatory region 8031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181065969-181066485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1605 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:181074489-181075383 Neighboring gene immediate early response 5 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:181080957-181082156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2175 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2179 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:181103703-181104902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1608 Neighboring gene VISTA enhancer hs1862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2184 Neighboring gene Sharpr-MPRA regulatory region 5219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1610 Neighboring gene long intergenic non-protein coding RNA 1732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181151125-181151624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181176185-181177094 Neighboring gene long intergenic non-protein coding RNA 1699

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  5. 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

  • ATAC-STARR-seq lymphoblastoid active region 2182
  • CRISPRi-validated cis-regulatory element chr1.10177
  • H3K4me1 hESC enhancer GRCh37_chr1:181110258-181110758
  • H3K4me1 hESC enhancer GRCh37_chr1:181110759-181111259

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_066116.2 

    Range
    101..1102
    Download
    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
    181141122..181142123
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    180496556..180497557
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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