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LOC111464991 H3K4me1 hESC enhancer GRCh37_chr1:41286429-41286930 [ Homo sapiens (human) ]

Gene ID: 111464991, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111464991
Gene description
H3K4me1 hESC enhancer GRCh37_chr1:41286429-41286930
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 predicted to be a cell type-specific enhancer 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 primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. Two overlapping subregions were also validated as enhancers by high-throughput massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. Each of those subregions contains two conserved motifs for a GATA activator, and mutation of either motif results in reduced enhancer activity. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (40820757..40821258)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (40689992..40690493)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (41286642..41286828)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nuclear transcription factor Y subunit gamma Neighboring gene ATAC-STARR-seq lymphoblastoid active region 853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 854 Neighboring gene microRNA 30c-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:41253587-41254086 Neighboring gene potassium voltage-gated channel subfamily Q member 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:41267963-41268147 Neighboring gene RNA, 7SL, cytoplasmic 326, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:41279047-41279546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 735 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:41290219-41291122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:41300271-41300796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:41305349-41305957 Neighboring gene uncharacterized LOC105378676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 736 Neighboring gene Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4

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. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Kheradpour P, et al. Genome Res, 2013 May. PMID 23512712, Free PMC Article
  2. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, et al. Nature, 2011 May 5. PMID 21441907, Free PMC Article
  3. 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

  • GATA activator MPRA enhancer 242
  • GATA activator MPRA enhancer 247
  • GATA motif-containing MPRA enhancers 242 and 247
  • massively parallel reporter assay enhancers 242 and 247

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_055907.2 

    Range
    101..602
    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
    40820757..40821258
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    40689992..40690493
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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