U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC116276485 CRISPRi-validated cis-regulatory element chr17.6006 [ Homo sapiens (human) ]

Gene ID: 116276485, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC116276485
Gene description
CRISPRi-validated cis-regulatory element chr17.6006
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 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 cis-regulatory element for the RAC3 (Rac family small GTPase 3) gene on chromosome 17 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 (MPRA) in naive 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (81483629..81484980)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82400641..82401992)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (79451209..79452006)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene BAH domain and coiled-coil containing 1 Neighboring gene uncharacterized LOC124904084 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79422900-79423848 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79423849-79424797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79438477-79438978 Neighboring gene long intergenic non-protein coding RNA 1971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9127 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79455547-79456267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79456989-79457708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79460397-79460898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79466919-79467642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9128 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79482073-79482696 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79482697-79483322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12967 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79483947-79484572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79484573-79485196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12970 Neighboring gene actin gamma 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79495325-79495851 Neighboring gene fascin actin-bundling protein 2, retinal Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79495852-79496377

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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. 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
  5. 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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 9126
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79450655-79451305

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_067036.2 

    Range
    101..1452
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    81483629..81484980
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791805.1 Reference GRCh38.p14 PATCHES

    Range
    139834..141185
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    82400641..82401992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases