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LOC128462388 CRISPRi-FlowFISH-validated PPIF regulatory element GRCh37_chr10:81044989-81045489 [ Homo sapiens (human) ]

Gene ID: 128462388, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128462388
Gene description
CRISPRi-FlowFISH-validated PPIF regulatory element GRCh37_chr10:81044989-81045489
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 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. A subregion was validated as a positively-acting cis-regulatory element for the PPIF (peptidylprolyl isomerase F) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in GM12878 lymphoblastoid cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC128462388 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (79285232..79285757)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (80154573..80155098)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80491819-80492320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80492321-80492820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80516074-80516712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80517991-80518628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80517352-80517990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80527882-80528481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80536737-80537624 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:80561226-80561763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80587578-80588078 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80611199-80611786 Neighboring gene NANOG hESC enhancer GRCh37_chr10:80619958-80620464 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:80635056-80635704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80660163-80660663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80670266-80670770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80670771-80671275 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:80673020-80673539 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80673540-80674060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80675693-80676194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80676195-80676694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80696869-80697391 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80715276-80715991 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80724486-80725046 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:80726805-80727304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80727311-80728094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80731917-80732848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3619 Neighboring gene ZMIZ1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80739778-80740278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80740279-80740779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3620 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:80742018-80742209 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80756413-80756912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80768616-80769116 Neighboring gene uncharacterized LOC112268062 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory element GRCh37_chr10:80782948-80783448 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:80806812-80808011 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80808619-80809301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80814153-80814652 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2524 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80827637-80828482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3623 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80832039-80832542 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80839841-80840350 Neighboring gene hESC enhancers GRCh37_chr10:80843535-80844106 and GRCh37_chr10:80844107-80844676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80847474-80848460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80848461-80849447 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80850069-80850570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80850571-80851070 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:80853442-80853942 and GRCh37_chr10:80853471-80853971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80856811-80857382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80861855-80862738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80860971-80861854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80862739-80863620 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:80867111-80867288 Neighboring gene HNF1 motif-containing MPRA enhancer 157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80872521-80873111 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80873112-80873701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80873702-80874292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80874293-80874881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2529 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80886414-80886932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80889167-80889808 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory element GRCh37_chr10:80892363-80892863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80897004-80897684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80904675-80905613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3627 Neighboring gene zinc finger MIZ-type containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2531 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80915969-80916820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80918523-80919372 Neighboring gene HNF1 motif-containing MPRA enhancer 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80922057-80922728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80930785-80931574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80937580-80938196 Neighboring gene Sharpr-MPRA regulatory region 270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80938197-80938813 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80941281-80941897 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:80943423-80944622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80944822-80945581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80947279-80947814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80947815-80948349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80949957-80950491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80961241-80961741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80960740-80961240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:80969381-80970255 Neighboring gene VISTA enhancer hs1767 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80984385-80985122 Neighboring gene Sharpr-MPRA regulatory region 8427 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80996160-80996788 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80996789-80997417 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80999304-80999932 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:80999933-81000560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:81001601-81002552 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81003385-81003885 and GRCh37_chr10:81003389-81003889 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory element GRCh37_chr10:81004281-81005113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3634 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2537 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81007811-81008725 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81008726-81009639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81015755-81016750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81016751-81017746 Neighboring gene Sharpr-MPRA regulatory region 1120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81023533-81024492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:81025451-81026410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:81033176-81034046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81034047-81034918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81034919-81035789 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:81039443-81039612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3639 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr10:81046379-81047029 and GRCh37_chr10:81045728-81046378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2538 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81053513-81054274 and GRCh37_chr10:81053559-81054389 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:81064163-81065362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81072795-81073294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81071537-81072037 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81076336-81076836 to GRCh37_chr10:81076368-81076868 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81077051-81077551 to GRCh37_chr10:81077572-81078072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:81078090-81078665 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81080832-81081332 to GRCh37_chr10:81080873-81081373 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81082504-81083416 to GRCh37_chr10:81082920-81083420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3643 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81088372-81088872 to GRCh37_chr10:81088582-81089082 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:81091043-81092242 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81106892-81107469 to GRCh37_chr10:81107706-81108206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81108973-81109473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81111476-81111976 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81112809-81113784 to GRCh37_chr10:81113845-81114345 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory element GRCh37_chr10:81115805-81116305 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81134127-81134627 and GRCh37_chr10:81134130-81134914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:81135469-81136005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81145819-81146746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81150060-81150645 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory element GRCh37_chr10:81159191-81159691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81162702-81163510 Neighboring gene CRISPRi-FlowFISH-validated PPIF regulatory elements GRCh37_chr10:81163946-81164446 and GRCh37_chr10:81163953-81164453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81165127-81165934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81172654-81173164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81173165-81173673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81184235-81184736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2541 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:81194851-81195489 Neighboring gene peptidylprolyl isomerase F Neighboring gene zinc finger CCHC-type containing 24

Genomic regions, transcripts, and products

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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
  2. 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

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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 3640

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_149576.2 

    Range
    101..626
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    79285232..79285757
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    80154573..80155098
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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