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LOC130004225 ATAC-STARR-seq lymphoblastoid silent region 2557 [ Homo sapiens (human) ]

Gene ID: 130004225, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004225
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2557
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence represents an accessible chromatin region 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC130004225 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (86366284..86366483)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (87246817..87247016)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (88126041..88126240)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene glutamate ionotropic receptor delta type subunit 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:87818313-87818519 Neighboring gene RNA, 5S ribosomal pseudogene 322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:87851089-87851613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:87864301-87864801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:87894862-87895400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:87938293-87938794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:87938795-87939294 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:87965696-87966220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:87966221-87966744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:87986763-87987262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:87992997-87993662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88021719-88022702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88022703-88023686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88024064-88024564 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17795 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88051161-88051975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88051976-88052790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88057946-88058446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88089455-88090419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88091551-88092052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88092053-88092552 Neighboring gene microRNA 346 Neighboring gene Sharpr-MPRA regulatory region 9256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88123147-88123660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88122633-88123146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2558 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88136831-88137373 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2563 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88160525-88161518 Neighboring gene uncharacterized LOC124902473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88159531-88160524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88162319-88162871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3689 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88183258-88184012 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17841 Neighboring gene Sharpr-MPRA regulatory region 10398 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88221644-88222250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3691 Neighboring gene RNA, U6 small nuclear 780, pseudogene Neighboring gene WAPL cohesin release factor

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

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_183671.1 

    Range
    101..300
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    86366284..86366483
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    87246817..87247016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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