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LOC111413040 FOXA motif-containing MPRA enhancer 183 [ Homo sapiens (human) ]

Gene ID: 111413040, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111413040
Gene description
FOXA motif-containing MPRA enhancer 183
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 (137354059..137354203)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (138542512..138542656)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (137675196..137675340)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17580 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:137540162-137540892 Neighboring gene interferon gamma receptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25139 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:137618853-137619479 Neighboring gene uncharacterized LOC105378017 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:137636227-137636827 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:137672426-137672621 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90385 Neighboring gene uncharacterized LOC102723633 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:137744471-137745316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:137808523-137809198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:137814441-137814940 Neighboring gene oligodendrocyte transcription factor 3

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 183
  • massively parallel reporter assay enhancer 183

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_055870.1 

    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
    137354059..137354203
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    138542512..138542656
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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