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LOC128462395 CRISPRi-FlowFISH-validated IL6ST regulatory element GRCh37_chr5:55444297-55444797 [ Homo sapiens (human) ]

Gene ID: 128462395, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128462395
Gene description
CRISPRi-FlowFISH-validated IL6ST regulatory element GRCh37_chr5:55444297-55444797
Gene type
biological region
Feature type(s)
regulatory: 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 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 the IL6ST (interleukin 6 cytokine family signal transducer) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in Jurkat T cells. This biological region may be relevant for coronavirus biology because the IL6ST target gene is involved in immune response or antiviral activity. [provided by RefSeq, Feb 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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See LOC128462395 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (56148470..56148970)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (56975753..56976254)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ankyrin repeat domain 55 Neighboring gene ribosomal protein L17 pseudogene 22 Neighboring gene RNA, 5S ribosomal pseudogene 184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16019 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:55452705-55453500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:55455891-55456686 Neighboring gene Sharpr-MPRA regulatory region 5241 Neighboring gene C1GALT1 pseudogene 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:55535983-55537182 Neighboring gene NANOG hESC enhancer GRCh37_chr5:55553446-55553953 Neighboring gene RNA, 5S ribosomal pseudogene 185

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

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

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_149583.1 

    Range
    101..601
    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
    56148470..56148970
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    56975753..56976254
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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