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LOC113748397 H3K4me1 hESC enhancers GRCh37_chr7:50569579-50570080 and GRCh37_chr7:50570081-50570580 [ Homo sapiens (human) ]

Gene ID: 113748397, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113748397
Gene description
H3K4me1 hESC enhancers GRCh37_chr7:50569579-50570080 and GRCh37_chr7:50570081-50570580
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. Two subregions marked by the H3K4me1 histone modification were validated as active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. An overlapping subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC113748397 in Genome Data Viewer
Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (50501881..50502882)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (50663105..50664106)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (50570049..50570343)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1091, pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:50514049-50515248 Neighboring gene Sharpr-MPRA regulatory region 9826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18183 Neighboring gene fidgetin like 1 Neighboring gene VISTA enhancer hs2059 Neighboring gene dopa decarboxylase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:50581285-50581919 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_99424 and experimental_99425 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:50598907-50600106 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:50602470-50603669 Neighboring gene DDC antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:50637965-50638490 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99443 Neighboring gene growth factor receptor bound protein 10 Neighboring gene uncharacterized LOC124901632

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. The DNA sequence of human chromosome 7. Hillier LW, et al. Nature, 2003 Jul 10. PMID 12853948
  2. 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
  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

  • H3K4me1 hESC enhancer GRCh37_chr7:50569579-50570080
  • H3K4me1 hESC enhancer GRCh37_chr7:50570081-50570580
  • Sharpr-MPRA regulatory region 9793

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_062508.2 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    50501881..50502882
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    50663105..50664106
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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