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LOC111413030 FOXA motif-containing MPRA enhancer 167 [ Homo sapiens (human) ]

Gene ID: 111413030, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111413030
Gene description
FOXA motif-containing MPRA enhancer 167
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 high-throughput massively parallel reporter assays (MPRAs) in liver carcinoma HepG2 cells. This enhancer contains a conserved motif for the FOXA activator. Mutation of this motif results in reduced enhancer activity. [provided by RefSeq, Nov 2017]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (87785329..87785473)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (88993675..88993819)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (88495047..88495191)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene origin recognition complex subunit 3 Neighboring gene NANOG hESC enhancer GRCh37_chr6:88408207-88408726 Neighboring gene akirin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24802 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24805 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:88445010-88445674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24808 Neighboring gene uncharacterized LOC101928911 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:88505589-88506090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:88506091-88506590 Neighboring gene NANOG hESC enhancer GRCh37_chr6:88508442-88508943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24810 Neighboring gene RNA, 7SL, cytoplasmic 183, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:88571406-88572219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24812 Neighboring gene CAGE-defined B cell enhancer in LOC101928911-SPACA1 intergenic region Neighboring gene uncharacterized LOC105377882

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

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 167
  • massively parallel reporter assay enhancer 167

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_055861.1 

    Range
    101..245
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    87785329..87785473
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    88993675..88993819
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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