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LOC127405237 NANOG-H3K4me1 hESC enhancer GRCh37_chr6:5639236-5640099 [ Homo sapiens (human) ]

Gene ID: 127405237, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127405237
Gene description
NANOG-H3K4me1 hESC enhancer GRCh37_chr6:5639236-5640099
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 region was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K4me1 histone modification. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC127405237 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (5639003..5639866)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (5508294..5509157)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (5639236..5640099)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene phenylalanyl-tRNA synthetase 2, mitochondrial Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5456946-5457932 Neighboring gene FARS2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23907 Neighboring gene MPRA-validated peak5636 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23908 Neighboring gene NANOG hESC enhancer GRCh37_chr6:5529614-5530223 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:5541695-5542894 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:5581546-5582745 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 37 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23910 Neighboring gene uncharacterized LOC101927950 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:5665450-5666649 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:5672975-5673971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23912 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:5737751-5738252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5783313-5783996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5783997-5784680 Neighboring gene ribosomal protein L34 pseudogene 16

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ReSE screen-validated silencer GRCh37_chr6:5639845-5640065

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_107208.1 

    Range
    101..964
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    5639003..5639866
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    5508294..5509157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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