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LOC111365201 FOXA motif-containing MPRA enhancer 78 [ Homo sapiens (human) ]

Gene ID: 111365201, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111365201
Gene description
FOXA motif-containing MPRA enhancer 78
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. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). A sub-region was also validated as a functional enhancer by high-throughput massively parallel reporter assays (MPRAs) in HepG2 cells. The sub-region contains a conserved motif for the FOXA activator, and mutation of the motif results in reduced enhancer activity. [provided by RefSeq, May 2018]
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Genomic context

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Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (57446057..57446351)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (57646930..57647224)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (55113289..55113583)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 737, pseudogene Neighboring gene ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:55101332-55101912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:55101913-55102492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:55104607-55105362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:55106119-55106874 Neighboring gene one cut homeobox 2 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_48194 and experimental_48198 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48219 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13370 Neighboring gene MPRA-validated peak3163 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr18:55230082-55230255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13373 Neighboring gene ferrochelatase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9481 Neighboring gene Sharpr-MPRA regulatory region 4588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:55288917-55289621 Neighboring gene asparaginyl-tRNA synthetase 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

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

  • FOXA activator MPRA enhancer 78
  • Sharpr-MPRA regulatory region 10477
  • massively parallel reporter assay enhancer 78

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_055816.2 

    Range
    101..395
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    57446057..57446351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    57646930..57647224
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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