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LOC127272199 NANOG hESC enhancer GRCh37_chr1:246228833-246229369 [ Homo sapiens (human) ]

Gene ID: 127272199, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127272199
Gene description
NANOG hESC enhancer GRCh37_chr1:246228833-246229369
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 in primed human embryonic stem cells. This enhancer associates with the NANOG transcription factor. [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (246065531..246066067)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (245486356..245486892)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene kinesin family member 26B Neighboring gene uncharacterized LOC124904571 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:245746285-245747484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245769345-245770175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245774720-245775220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245775221-245775721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245786008-245786527 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245811797-245812310 Neighboring gene uncharacterized LOC105373265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245874821-245875320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245874319-245874820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245878266-245878766 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:245926173-245926700 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245937857-245938697 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245938698-245939538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2851 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245980136-245980750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245979520-245980135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246016290-246016790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246016791-246017291 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:246032999-246034198 Neighboring gene SET and MYND domain containing 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246111472-246111972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:246226795-246227321 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246273353-246273854 Neighboring gene Sharpr-MPRA regulatory region 4643 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246273855-246274354 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:246302792-246303991 Neighboring gene CRISPRi-validated SMYD3 hub enhancer Neighboring gene SMYD3 antisense RNA 1 Neighboring gene CRISPRi-validated SMYD3 non-hub enhancer Neighboring gene CRISPR perturbation-validated SMYD3 cis-regulatory element TAD4.SE2.HS8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2030 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 4 pseudogene 5

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. 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

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_094050.1 

    Range
    101..637
    Download
    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
    246065531..246066067
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    245486356..245486892
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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