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LOC127405145 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2989763-2990572 [ Homo sapiens (human) ]

Gene ID: 127405145, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127405145
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2989763-2990572
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 region was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. 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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See LOC127405145 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (2989529..2990338)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (2858425..2859261)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene SERPINB9 antisense RNA 1 Neighboring gene MPRA-validated peak5624 silencer Neighboring gene serpin family B member 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16834 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2903007-2903508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16837 Neighboring gene hESC enhancers GRCh37_chr6:2907997-2908830 and GRCh37_chr6:2908831-2909664 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:2916616-2917158 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:2921833-2922334 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:2928364-2929022 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2929023-2929682 Neighboring gene serpin family B member 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2960063-2960678 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2971582-2972106 Neighboring gene SERPINB6-LINC01011 intergenic CAGE-defined mid-level expression enhancer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2988143-2988952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2988953-2989762 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2990573-2991380 Neighboring gene long intergenic non-protein coding RNA 1011 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:2994147-2994331 Neighboring gene NQO2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16839 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:3014049-3014548 Neighboring gene N-ribosyldihydronicotinamide:quinone dehydrogenase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3017263-3017764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3017765-3018264 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:3023471-3024670 Neighboring gene uncharacterized LOC101927759 Neighboring gene Sharpr-MPRA regulatory region 12329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23882 Neighboring gene HIV-1 Tat specific factor 1 pseudogene 2

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. 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
  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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 23880

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_107116.1 

    Range
    101..910
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    2989529..2990338
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    2858425..2859261
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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