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LOC121627844 H3K4me1 hESC enhancer GRCh37_chr19:1361729-1362399 [ Homo sapiens (human) ]

Gene ID: 121627844, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627844
Gene description
H3K4me1 hESC enhancer GRCh37_chr19:1361729-1362399
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 naive 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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC121627844 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 (1361730..1362400)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (1331706..1332376)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1362029..1362323)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1284956-1285456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1285457-1285957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1287962-1288548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1291327-1292207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1293760-1294329 Neighboring gene ephrin A2 Neighboring gene ribosomal protein S15 pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9700 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:1324501-1325014 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:1325015-1325526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1354759-1355644 Neighboring gene PWWP domain containing 3A, DNA repair factor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1368468-1368968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1368969-1369469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1380436-1380936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9705 Neighboring gene tRNA-Phe (anticodon GAA) 1-6 Neighboring gene tRNA-Asn (anticodon GTT) 2-6

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 14028

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_075035.2 

    Range
    101..771
    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
    1361730..1362400
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    1331706..1332376
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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