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LOC127275229 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172291003-172291562 [ Homo sapiens (human) ]

Gene ID: 127275229, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127275229
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172291003-172291562
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 region includes an enhancer that was validated 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 and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC127275229 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (171433984..171435052)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (171911124..171912192)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (172290494..172291562)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373737 Neighboring gene small integral membrane protein 26-like Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:172172370-172173192 Neighboring gene Sharpr-MPRA regulatory region 707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16746 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:172174870-172175072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16747 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172175660-172176482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16748 Neighboring gene Sharpr-MPRA regulatory region 8774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16750 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:172183340-172183864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12100 Neighboring gene methyltransferase 8, tRNA N3-cytidine Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16751 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172242874-172243458 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172243459-172244043 Neighboring gene ribosomal protein S26 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16756 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr2:172289881-172290441 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:172303768-172303972 Neighboring gene DDB1 and CUL4 associated factor 17 Neighboring gene CRISPRi-validated cis-regulatory element chr2.5458 Neighboring gene death associated protein 3 pseudogene 2 Neighboring gene ribosomal protein S15 pseudogene 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 12102

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_097077.2 

    Range
    101..1169
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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
    171433984..171435052
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    171911124..171912192
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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