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LOC111519898 HNF1 motif-containing MPRA enhancer 93 [ Homo sapiens (human) ]

Gene ID: 111519898, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111519898
Gene description
HNF1 motif-containing MPRA enhancer 93
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. A sub-region was validated as a functional enhancer by high-throughput massively parallel reporter assays (MPRAs) in both HepG2 liver carcinoma cells and K562 erythroleukemia cells. This sub-region contains a motif for the HNF1 activator, and mutation of the motif results in reduced enhancer activity. This genomic region was also validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using MPRAs) in both HepG2 cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 cells (group: K562 Activating DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jul 2018]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (37569442..37569736)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (38030704..38030998)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (37965449..37965743)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37898069-37898668 Neighboring gene caspase recruitment domain family member 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37898669-37899266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37904132-37904960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37904961-37905787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37907945-37908458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37934271-37934772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37934773-37935272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37948043-37948624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37948625-37949206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37957123-37957729 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37957730-37958337 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37958338-37958944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37959472-37959972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37959973-37960473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37963831-37964482 Neighboring gene CDC42 effector protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37965972-37966480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37967120-37967620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37967621-37968121 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13687 Neighboring gene galectin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18977 Neighboring gene Sharpr-MPRA regulatory region 7746 Neighboring gene CRISPRi-validated cis-regulatory element chr22.1757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38005225-38005846 Neighboring gene golgi associated, gamma adaptin ear containing, ARF binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38029311-38030184

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

  • HNF1 activator MPRA enhancer 93
  • Sharpr-MPRA regulatory region 9066
  • massively parallel reporter assay enhancer 93

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_055950.2 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    37569442..37569736
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    38030704..38030998
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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