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LOC108251791 FAM174B-LINC01578 intergenic CAGE-defined high expression enhancer [ Homo sapiens (human) ]

Gene ID: 108251791, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108251791
Gene description
FAM174B-LINC01578 intergenic CAGE-defined high expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
regulatory: enhancer, silencer, 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 element is located in the intergenic region between the FAM174B (family with sequence similarity 174 member B) and LINC01578 (long intergenic non-protein coding RNA 1578) genes. A subregion was defined as a high expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE), and was validated as an enhancer by reporter assays in both HeLa and HepG2 cells. A subregion was also validated as an enhancer by high-throughput massively parallel reporter assays (MPRAs) in HepG2 cells. That subregion contains a conserved motif for the ZFP161 transcription factor, and mutation of the motif results in reduced enhancer activity. A different subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using MPRAs) in HepG2 cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). Another subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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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See LOC108251791 in Genome Data Viewer
Location:
15q26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (92820234..92821060)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (90582498..90583324)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (93363464..93364154)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93344283-93345134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10118 Neighboring gene uncharacterized LOC124903558 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93351993-93352843 Neighboring gene ankyrin repeat and SOCS box containing 9 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93368032-93368688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10121 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10125 Neighboring gene MPRA-validated peak2429 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10127 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:93425915-93426556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6849 Neighboring gene CHD2 adjacent suppressive regulatory RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10129 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:93447162-93448361 Neighboring gene microRNA 3175 Neighboring gene chromodomain helicase DNA binding protein 2

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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
  2. 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
  3. 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
  4. 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
  5. 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

See all (6) citations in PubMed

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 silent region 6847
  • FAM174B-LINC01578 interval high CAGE FANTOM5 enhancer
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93363625-93364290
  • Sharpr-MPRA regulatory region 396
  • ZFP161 motif-containing MPRA enhancer 236/237
  • massively parallel reporter assay enhancer 236/237

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_050992.2 

    Range
    101..927
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    92820234..92821060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    90582498..90583324
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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