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LOC127890560 H3K4me1 hESC enhancer GRCh37_chr19:13210189-13211052 [ Homo sapiens (human) ]

Gene ID: 127890560, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127890560
Gene description
H3K4me1 hESC enhancer GRCh37_chr19:13210189-13211052
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 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. 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) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC127890560 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13099375..13100238)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13224589..13225452)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13210189..13211052)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13079936-13080539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13080540-13081142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13085246-13085752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10187 Neighboring gene DAN domain BMP antagonist family member 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13095227-13095752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13106570-13107158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13121583-13122126 Neighboring gene nuclear factor I X Neighboring gene uncharacterized LOC107985286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13134224-13134736 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13135703-13136522 Neighboring gene VISTA enhancer hs1900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13168092-13168678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13170695-13171596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13171597-13172496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13187265-13188200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10189 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13206733-13207596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14106 Neighboring gene CRISPRi-FlowFISH-validated CALR, DNASE2 and KLF1 regulatory element Neighboring gene Sharpr-MPRA regulatory region 14065 Neighboring gene uncharacterized LOC105372282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13220465-13220965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14109 Neighboring gene LYL1 basic helix-loop-helix family member Neighboring gene tRNA methyltransferase 1

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 14105

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_140486.1 

    Range
    101..964
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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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    13099375..13100238
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    13224589..13225452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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