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LOC121853014 H3K4me1 hESC enhancer GRCh37_chr20:55989747-55990514 [ Homo sapiens (human) ]

Gene ID: 121853014, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853014
Gene description
H3K4me1 hESC enhancer GRCh37_chr20:55989747-55990514
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). Another subregion represents a red blood cell enhancer that was functionally validated by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. It includes rs737092, an MPRA functional variant (MFV) that affects activity of that enhancer. Deletions encompassing the MFV, which were obtained by CRISPR/Cas9 editing, indicate this region is a positively-acting cis-regulatory element for the RAE1 (ribonucleic acid export 1) and RBM38 (RNA binding motif protein 38) genes in K562 cells. [provided by RefSeq, Feb 2023]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (57414691..57415458)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (59192449..59193216)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (55990109..55990403)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ribonucleic acid export 1 Neighboring gene uncharacterized LOC124904938 Neighboring gene Sharpr-MPRA regulatory region 7479 Neighboring gene RBM38 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13059 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55966169-55966670 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55966671-55967170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55970944-55971905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55973481-55973980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55975022-55975885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18148 Neighboring gene RNA binding motif protein 38 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55984023-55984528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18149 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:55985201-55985370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55988977-55989746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55990515-55991283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18154 Neighboring gene uncharacterized LOC124904939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18155 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:56012611-56012842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56014209-56014710 Neighboring gene VISTA enhancer hs1971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18156 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr20:56026537-56027036 and GRCh37_chr20:56027096-56027596 Neighboring gene uncharacterized LOC105372688 Neighboring gene Sharpr-MPRA regulatory region 5175

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. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits. Ulirsch JC, et al. Cell, 2016 Jun 2. PMID 27259154, Free PMC Article
  2. Genome-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, Free PMC Article
  3. 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
  4. 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

  • CRISPRi-validated RAE1 and RBM38 regulatory element
  • MPRA functional variant 20:55990405:T:C red blood cell enhancer
  • Sharpr-MPRA regulatory region 4494

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_076122.2 

    Range
    101..868
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    57414691..57415458
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    59192449..59193216
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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