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LOC121725022 NANOG-H3K27ac hESC enhancers GRCh37_chr1:52815874-52816848 and GRCh37_chr1:52816849-52817822 [ Homo sapiens (human) ]

Gene ID: 121725022, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725022
Gene description
NANOG-H3K27ac hESC enhancers GRCh37_chr1:52815874-52816848 and GRCh37_chr1:52816849-52817822
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 associated with the NANOG transcription factor and marked by the H3K27ac histone modification were shown to be 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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC121725022 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (52350202..52352150)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (52231667..52233615)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (52816649..52816943)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene zinc finger FYVE-type containing 9 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 pseudogene 7 Neighboring gene anaphase promoting complex subunit 10 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:52822843-52823344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 886 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 889 Neighboring gene coiled-coil and C2 domain containing 1B Neighboring gene phospholipase A2 group XIIA pseudogene 1 Neighboring gene origin recognition complex subunit 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:52869594-52870793 Neighboring gene pre-mRNA processing factor 38A

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

  • NANOG-H3K27ac hESC enhancer GRCh37_chr1:52815874-52816848
  • NANOG-H3K27ac hESC enhancer GRCh37_chr1:52816849-52817822
  • Sharpr-MPRA regulatory region 8197

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_075492.2 

    Range
    101..2049
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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
    52350202..52352150
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    52231667..52233615
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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