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LOC120961750 H3K4me1 hESC enhancer GRCh37_chr2:43396769-43397414 [ Homo sapiens (human) ]

Gene ID: 120961750, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120961750
Gene description
H3K4me1 hESC enhancer GRCh37_chr2:43396769-43397414
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. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (43169630..43170275)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (43174923..43175568)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (43397089..43397383)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43327965-43328636 Neighboring gene long intergenic non-protein coding RNA 2580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43354504-43355004 Neighboring gene uncharacterized LOC105374570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43360411-43361174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43361175-43361936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43367134-43367705 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43367706-43368276 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43379975-43380123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43384913-43385431 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43385646-43385841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43394830-43395476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43397590-43398275 Neighboring gene uncharacterized LOC124907755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43404972-43405498 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1717 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:43407075-43407600 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:43411165-43412364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43412481-43413214 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43413949-43414682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43414683-43415416 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43421149-43422068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43437212-43437806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43441787-43442553 Neighboring gene VISTA enhancer hs1909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11423 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:43453393-43454356 Neighboring gene ZFP36 ring finger protein like 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

  • Sharpr-MPRA regulatory region 1558

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_073967.2 

    Range
    101..746
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    43169630..43170275
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    43174923..43175568
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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