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LOC121627857 H3K4me1 hESC enhancer GRCh37_chr19:14515967-14516596 [ Homo sapiens (human) ]

Gene ID: 121627857, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627857
Gene description
H3K4me1 hESC enhancer GRCh37_chr19:14515967-14516596
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 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 K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC121627857 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (14405155..14405784)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (14531829..14532458)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (14516169..14516463)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr19:14328052-14328362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14332061-14332584 Neighboring gene RNA, 7SL, cytoplasmic 231, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14360564-14361081 Neighboring gene MPRA-validated peak3380 silencer Neighboring gene MPRA-validated peak3381 silencer Neighboring gene Sharpr-MPRA regulatory region 1520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14408885-14409384 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:14421820-14422074 Neighboring gene long intergenic non-protein coding RNA 1841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14429209-14429710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14429711-14430210 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14444577-14445252 Neighboring gene MPRA-validated peak3382 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14449292-14449792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14449793-14450293 Neighboring gene long intergenic non-protein coding RNA 1842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14459126-14460004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14460803-14461304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14461305-14461804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14162 Neighboring gene Sharpr-MPRA regulatory region 7322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14163 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10244 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:14507248-14508447 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:14512346-14513545 Neighboring gene adhesion G protein-coupled receptor E5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14516597-14517226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10247 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10248 Neighboring gene DExD-box helicase 39A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14169 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14544012-14544585 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14544586-14545158 Neighboring gene Sharpr-MPRA regulatory region 2073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14555029-14555529 Neighboring gene Sharpr-MPRA regulatory region 3261 Neighboring gene protein kinase N1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14582511-14583159

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 8500

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_075048.2 

    Range
    101..730
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    14405155..14405784
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    14531829..14532458
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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