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LOC130000278 ATAC-STARR-seq lymphoblastoid silent region 19144 [ Homo sapiens (human) ]

Gene ID: 130000278, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130000278
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19144
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 LOC130000278 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (41577927..41578546)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (41851685..41852304)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (41435446..41436065)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27287 Neighboring gene GPAT4 and GINS4 antisense RNA 1 Neighboring gene uncharacterized LOC124901939 Neighboring gene GINS complex subunit 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:41424977-41425739 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:41430689-41430895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:41451733-41452234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:41454165-41454665 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:41466108-41467307 Neighboring gene glycerol-3-phosphate acyltransferase 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19146 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:41510853-41511646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:41513473-41514006 Neighboring gene NK6 homeobox 3 Neighboring gene microRNA 486-1 Neighboring gene microRNA 486-2 Neighboring gene ankyrin 1

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_179724.1 

    Range
    101..720
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    41577927..41578546
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    41851685..41852304
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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