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LOC127399417 NANOG hESC enhancer GRCh37_chr3:186888631-186889132 [ Homo sapiens (human) ]

Gene ID: 127399417, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127399417
Gene description
NANOG hESC enhancer GRCh37_chr3:186888631-186889132
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 naive 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: 3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (187170843..187171344)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (189988271..189988772)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ST6 beta-galactoside alpha-2,6-sialyltransferase 1 Neighboring gene uncharacterized LOC124906314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20949 Neighboring gene Sharpr-MPRA regulatory region 11729 Neighboring gene Sharpr-MPRA regulatory region 4195 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20951 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186716158-186717048 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186717049-186717939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20957 Neighboring gene ST6GAL1 promoter P2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20959 Neighboring gene ST6GAL1 promoter P1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20963 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14993 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186789896-186790855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:186854800-186855300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:186856490-186856996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14994 Neighboring gene ribosomal protein L39 pseudogene 19 Neighboring gene ribosomal protein L39 like Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186892851-186893682 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186893683-186894513 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:186894725-186895400 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:186898085-186898586 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186898587-186899086 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186899087-186899588 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186900591-186901090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186901091-186901592 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186903095-186904094 Neighboring gene uncharacterized LOC101929106 Neighboring gene uncharacterized LOC105374260 Neighboring gene receptor transporter protein 1 Neighboring gene MBL associated serine protease 1

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_101383.1 

    Range
    101..602
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    187170843..187171344
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    189988271..189988772
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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