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LOC111365159 H3K4me1 hESC enhancers GRCh37_chr20:56026537-56027036 and GRCh37_chr20:56027096-56027596 [ Homo sapiens (human) ]

Gene ID: 111365159, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111365159
Gene description
H3K4me1 hESC enhancers GRCh37_chr20:56026537-56027036 and GRCh37_chr20:56027096-56027596
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 region was predicted to be a cell type-specific enhancer based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. Two subregions marked by the H3K4me1 histone modification were validated as active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. Another subregion was validated as an enhancer by high-throughput massively parallel reporter assays (MPRAs) in both liver carcinoma HepG2 cells and erythroleukemia K562 cells. That subregion contains a conserved motif for a GATA activator, and mutation of the motif results in reduced enhancer activity. An overlapping subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using MPRAs) in both HepG2 cells (group: HepG2 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched) and K562 cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (57451481..57452540)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (59229301..59230360)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (56026989..56027283)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RBM38 antisense RNA 1 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 H3K4me1 hESC enhancer GRCh37_chr20:55989747-55990514 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 uncharacterized LOC105372688 Neighboring gene Sharpr-MPRA regulatory region 5175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56039390-56040220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56042501-56043002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56045653-56046391 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56048063-56048564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56048565-56049064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56051358-56051858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13063 Neighboring gene high mobility group box 1 pseudogene 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. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Kheradpour P, et al. Genome Res, 2013 May. PMID 23512712, Free PMC Article
  2. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, et al. Nature, 2011 May 5. PMID 21441907, 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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  5. 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

  • ATAC-STARR-seq lymphoblastoid active region 18157
  • GATA activator MPRA enhancer 47
  • GATA motif-containing MPRA enhancer 47
  • H3K4me1 hESC enhancer GRCh37_chr20:56026537-56027036
  • H3K4me1 hESC enhancer GRCh37_chr20:56027096-56027596
  • Sharpr-MPRA regulatory region 12455
  • massively parallel reporter assay enhancer 47

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_055733.3 

    Range
    101..1160
    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
    57451481..57452540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    59229301..59230360
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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