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LOC116276472 CRISPRi-validated cis-regulatory element chr17.3537 [ Homo sapiens (human) ]

Gene ID: 116276472, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116276472
Gene description
CRISPRi-validated cis-regulatory element chr17.3537
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 cis-regulatory element for both the LRRC59 (leucine rich repeat containing 59) and PHB1 (prohibitin 1) genes 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 in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (49860164..49861247)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (50723264..50724347)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (47937527..47937929)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:47879701-47880202 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:47880203-47880702 Neighboring gene SRP14 pseudogene 3 Neighboring gene lysine acetyltransferase 7 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:47893039-47894031 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:47911219-47911431 Neighboring gene uncharacterized LOC729220 Neighboring gene tachykinin precursor 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:47938611-47939558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:47941593-47942092 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:47942923-47943617 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:47948287-47949230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:47967128-47967965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:47967966-47968802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:47976271-47977012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:47980751-47981252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:47986569-47987069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:47990385-47990940 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:47991434-47992633 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:47993407-47993919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48001781-48002290 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:48005674-48006873 Neighboring gene MPRA-validated peak2887 silencer Neighboring gene MRT4 homolog, ribosome maturation factor pseudogene Neighboring gene RNA, U6 small nuclear 1313, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

  • H3K4me1 hESC enhancer GRCh37_chr17:47937661-47938610

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_067023.2 

    Range
    101..1184
    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
    49860164..49861247
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    50723264..50724347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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