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LOC115995512 CRISPRi-validated cis-regulatory element chr3.2860 [ Homo sapiens (human) ]

Gene ID: 115995512, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995512
Gene description
CRISPRi-validated cis-regulatory element chr3.2860
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 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. It was validated as a high-confidence cis-regulatory element for the RYBP (RING1 and YY1 binding protein) gene on chromosome 3 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 2019]
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Genomic context

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Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (72288827..72290063)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (72329324..72330560)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (72337978..72339214)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20074 Neighboring gene long intergenic non-protein coding RNA 870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20076 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:72226281-72226881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14526 Neighboring gene Sharpr-MPRA regulatory region 12200 Neighboring gene NANOG hESC enhancer GRCh37_chr3:72242807-72243499 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:72245432-72246000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:72252370-72252906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:72252907-72253442 Neighboring gene uncharacterized LOC124909393 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:72291263-72291470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20081 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20082 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:72318159-72319358 Neighboring gene uncharacterized LOC105377158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:72340695-72341195 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:72348604-72349803 Neighboring gene Sharpr-MPRA regulatory region 8765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20085 Neighboring gene uncharacterized LOC105377159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:72367959-72368500 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:72384094-72384660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14527 Neighboring gene MPRA-validated peak4695 silencer Neighboring gene RING1 and YY1 binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20086

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)

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_066593.1 

    Range
    101..1337
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    72288827..72290063
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    72329324..72330560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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