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LOC127402905 CRISPRi-FlowFISH-validated IL6ST regulatory element GRCh37_chr5:55289559-55291877 [ Homo sapiens (human) ]

Gene ID: 127402905, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127402905
Gene description
CRISPRi-FlowFISH-validated IL6ST regulatory element GRCh37_chr5:55289559-55291877
Gene type
biological region
Feature type(s)
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 region, which includes the 5' end of the IL6ST (interleukin 6 cytokine family signal transducer) gene, was predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. It was validated as a positively-acting cis-regulatory element for IL6ST based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in GM12878 lymphoblastoid cells. A subregion was also validated as an IL6ST positively-acting element by CRISPRi-FlowFISH in BJAB lymphoma cells, Jurkat T cells and THP-1 monocytic cells. This region is relevant for coronavirus biology because the IL6ST target gene is involved in immune response or antiviral activity. Another subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. 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 cells. [provided by RefSeq, May 2023]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is involved in host gene regulation.
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (55993731..55996049)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (56822151..56824473)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene DEAD-box helicase 4 Neighboring gene RNA, 5S ribosomal pseudogene 183 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:55098870-55099053 Neighboring gene heterogeneous nuclear ribonucleoprotein H1 pseudogene 3 Neighboring gene interleukin 31 receptor A Neighboring gene H3K4me1 hESC enhancers GRCh37_chr5:55198729-55199230 and GRCh37_chr5:55199231-55199730 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:55206646-55207845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:55218660-55219260 Neighboring gene interleukin 6 cytokine family signal transducer Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 5314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22561 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16018 Neighboring gene IL6ST divergent transcript Neighboring gene uncharacterized LOC105378976

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. Genome-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, Free PMC Article
  2. 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
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 16017
  • CRISPRi-FlowFISH-validated IL6ST regulatory element GRCh37_chr5:55290571-55291244
  • H3K27ac hESC enhancer GRCh37_chr5:55290833-55291344

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_104854.2 

    Range
    101..2419
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    55993731..55996049
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    56822151..56824473
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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