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LOC122756372 NANOG hESC enhancer GRCh37_chr2:8995048-8995599 [ Homo sapiens (human) ]

Gene ID: 122756372, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122756372
Gene description
NANOG hESC enhancer GRCh37_chr2:8995048-8995599
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. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it associates with the NANOG transcription factor. A subregion was also 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 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC122756372 in Genome Data Viewer
Location:
2p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (8854918..8855469)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (8878671..8879222)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (8995048..8995599)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8824708-8825498 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8825499-8826288 Neighboring gene inhibitor of DNA binding 2 Neighboring gene kinase D interacting substrate 220 Neighboring gene ARF like GTPase 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11129 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11130 Neighboring gene Sharpr-MPRA regulatory region 5743 Neighboring gene membrane bound O-acyltransferase domain containing 2 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 6065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11131 Neighboring gene uncharacterized LOC124907728

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

  • Sharpr-MPRA regulatory region 138

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_076861.2 

    Range
    101..652
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    8854918..8855469
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    8878671..8879222
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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