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LOC112577509 hESC enhancers GRCh37_chr1:164581219-164581760 and GRCh37_chr1:164581219-164581760 [ Homo sapiens (human) ]

Gene ID: 112577509, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577509
Gene description
hESC enhancers GRCh37_chr1:164581219-164581760 and GRCh37_chr1:164581219-164581760
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 were shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both subregions were marked by the H3K4me1 histone modification, and one subregion was additionally marked by H3K27ac. A 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (164611440..164612523)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (163957690..163958773)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (164581069..164581363)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene high mobility group box 3 pseudogene 6 Neighboring gene uncharacterized LOC124904759 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:164528003-164528502 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164559870-164560837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164561919-164562862 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:164571452-164572217 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:164572218-164572982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164578838-164579391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164579392-164579944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:164580135-164580676 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164581761-164582300 Neighboring gene PBX homeobox 1 Neighboring gene VISTA enhancer hs1202 Neighboring gene VISTA enhancer hs1235 Neighboring gene RNA, U6 small nuclear 171, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:164660437-164660937 Neighboring gene VISTA enhancer hs1144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1496 Neighboring gene Sharpr-MPRA regulatory region 1770 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:164704495-164705047 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:164717166-164718365 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:164728525-164729026 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:164729027-164729526 Neighboring gene PBX1 antisense RNA 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. 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164581219-164581760
  • H3K4me1 hESC enhancer GRCh37_chr1:164580677-164581218
  • Sharpr-MPRA regulatory region 14887

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_060225.2 

    Range
    101..1184
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    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
    164611440..164612523
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    163957690..163958773
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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