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LOC123575667 NANOG-H3K27ac hESC enhancer GRCh37_chr6:11126939-11127440 [ Homo sapiens (human) ]

Gene ID: 123575667, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575667
Gene description
NANOG-H3K27ac hESC enhancer GRCh37_chr6:11126939-11127440
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. A subregion 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 histone modification. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 16:ElonW, transcriptional elongation, weaker H3K36me3). Another subregion was identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. That subregion was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq MPRAs in K562 cells. [provided by RefSeq, Apr 2023]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (11126706..11127232)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (10994626..10995152)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (11127129..11127423)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ELOVL fatty acid elongase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:11045068-11045568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:11045569-11046069 Neighboring gene ELOVL2 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:11093674-11094214 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:11094215-11094756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16910 Neighboring gene endogenous retrovirus group FRD member 1, envelope Neighboring gene small integral membrane protein 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23978 Neighboring gene Sharpr-MPRA regulatory region 2452 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:11185257-11186456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11189930-11190701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11190702-11191472 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11195391-11196257 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11196258-11197123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23979 Neighboring gene uncharacterized LOC124901256 Neighboring gene neural precursor cell expressed, developmentally down-regulated 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16911 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23980 Neighboring gene Sharpr-MPRA regulatory region 1219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23983 Neighboring gene uncharacterized LOC105374925 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11298822-11299579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23984

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, Free PMC Article
  2. 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
  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

  • MPRA-validated peak5657 silencer
  • Sharpr-MPRA regulatory region 3750

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_077926.3 

    Range
    101..627
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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
    11126706..11127232
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    10994626..10995152
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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