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LOC121392921 NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:61559319-61560296 and GRCh37_chr11:61560297-61561272 [ Homo sapiens (human) ]

Gene ID: 121392921, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121392921
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:61559319-61560296 and GRCh37_chr11:61560297-61561272
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. Two subregions were validated as active enhancers by ChIP-STARR-seq in naive and primed human embryonic stem cells, where both are associated with the NANOG transcription factor and are marked by the H3K27ac and H3K4me1 histone modifications. An overlapping subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss). [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (61791847..61793800)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (61780764..61782717)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (61560089..61560383)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61450060-61450734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61450735-61451408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61457781-61458312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61458313-61458844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61462250-61462775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61462776-61463302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61463303-61463829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61465411-61465936 Neighboring gene diacylglycerol lipase alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61465937-61466463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61466990-61467516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61467517-61468042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61468570-61469095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61482486-61483272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61483273-61484058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61484845-61485630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61485631-61486417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61486418-61487203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61487991-61488775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61507907-61508480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61514637-61515498 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61516359-61517220 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3397 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3398 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:61523524-61524723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61524877-61525520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61528511-61529267 Neighboring gene MYRF antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61535574-61536150 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61536151-61536726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4800 Neighboring gene myelin regulatory factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61546818-61547486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61548157-61548825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61552558-61553302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61553303-61554047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61562818-61563318 Neighboring gene transmembrane protein 258 Neighboring gene microRNA 611 Neighboring gene flap structure-specific endonuclease 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3399 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61582779-61583676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3400 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3401 Neighboring gene fatty acid desaturase 1 Neighboring gene uncharacterized LOC124902680 Neighboring gene microRNA 1908 Neighboring gene fatty acid desaturase 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. 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

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61559319-61560296
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61560297-61561272
  • Sharpr-MPRA regulatory region 5973

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_074578.2 

    Range
    101..2054
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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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    61791847..61793800
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    61780764..61782717
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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