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LOC124174301 NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr8:101506997-101507937 and GRCh37_chr8:101507938-101508879 [ Homo sapiens (human) ]

Gene ID: 124174301, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124174301
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr8:101506997-101507937 and GRCh37_chr8:101507938-101508879
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 validated as active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where both are associated with the NANOG transcription factor and are marked by the H3K27ac and H3K4me1 histone modifications. An overlapping subregion was also validated as a functional repressive element 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 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). 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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Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (100494769..100496651)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (101620810..101622692)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (101507869..101508163)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27694 Neighboring gene microRNA 4471 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:101421928-101423127 Neighboring gene RNF19A-ANKRD46 intergenic CAGE-defined high expression enhancer Neighboring gene uncharacterized LOC124901990 Neighboring gene uncharacterized LOC105375670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27700 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:101455271-101456130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:101470299-101470976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:101471860-101472360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:101472361-101472861 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:101477753-101478339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27703 Neighboring gene uncharacterized LOC124901992 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:101499786-101500985 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:101503341-101504286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27708 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:101508880-101509820 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:101511587-101512088 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:101512089-101512588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:101522255-101522840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19418 Neighboring gene ankyrin repeat domain 46 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27713 Neighboring gene MPRA-validated peak7124 silencer Neighboring gene Sharpr-MPRA regulatory region 13822 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 62 Neighboring gene sorting nexin 31 Neighboring gene uncharacterized LOC105375671

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 27709
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:101506997-101507937
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:101507938-101508879
  • Sharpr-MPRA regulatory region 8717

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_078596.2 

    Range
    101..1983
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    100494769..100496651
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    101620810..101622692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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