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LOC116186928 CRISPRi-validated cis-regulatory element chr8.1663 [ Homo sapiens (human) ]

Gene ID: 116186928, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116186928
Gene description
CRISPRi-validated cis-regulatory element chr8.1663
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 represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. A subregion was validated as a high-confidence cis-regulatory element for the LYN (LYN proto-oncogene, Src family tyrosine kinase) gene on chromosome 8 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. Another subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (55847346..55848398)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (56224398..56225450)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (56760398..56760957)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 265 Neighboring gene transmembrane protein 68 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:56684839-56685342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27376 Neighboring gene trimethylguanosine synthase 1 Neighboring gene MPRA-validated peak7024 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27377 Neighboring gene Sharpr-MPRA regulatory region 11739 Neighboring gene Sharpr-MPRA regulatory region 4705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27381 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19205 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19204 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27383 Neighboring gene Sharpr-MPRA regulatory region 4485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:56827131-56827631 Neighboring gene LYN proto-oncogene, Src family tyrosine kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:56826630-56827130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27387 Neighboring gene Sharpr-MPRA regulatory region 838 Neighboring gene small nucleolar RNA, H/ACA box 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27388 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:56843083-56843621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:56852106-56852621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:56892491-56892991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:56893036-56893536 Neighboring gene RNA, 7SL, cytoplasmic 798, pseudogene

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:56759905-56760736

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_066848.2 

    Range
    101..1153
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    55847346..55848398
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    56224398..56225450
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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