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LOC130066604 ATAC-STARR-seq lymphoblastoid silent region 13277 [ Homo sapiens (human) ]

Gene ID: 130066604, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066604
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13277
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 LOC130066604 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (35046229..35046278)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (33429010..33429059)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (36418526..36418575)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:36208094-36209293 Neighboring gene RUNX family transcription factor 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:36237597-36238796 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:36239537-36240204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:36240205-36240870 Neighboring gene RUNX1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13274 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:36258151-36258922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:36258923-36259694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18408 Neighboring gene Sharpr-MPRA regulatory region 10978 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36332885-36333440 Neighboring gene Sharpr-MPRA regulatory region 10330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18412 Neighboring gene Sharpr-MPRA regulatory region 3099 Neighboring gene Sharpr-MPRA regulatory region 4684 Neighboring gene RUNX1 enhancer RE1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18417 Neighboring gene RUNX1 intronic transcript 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:36466332-36466488 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:36477528-36477706 Neighboring gene Sharpr-MPRA regulatory region 12281 Neighboring gene uncharacterized LOC124905015 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:36589399-36590598 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:36604354-36605553 Neighboring gene enhancer 4 sub-fragment of super-enhancer upstream of RUNX1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:36646465-36646966 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36743463-36743964 Neighboring gene uncharacterized LOC100506403 Neighboring gene Sharpr-MPRA regulatory region 14404 Neighboring gene Sharpr-MPRA regulatory region 5568 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36786783-36787398 Neighboring gene ribosomal protein L34 pseudogene 3

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_201021.1 

    Range
    101..150
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    35046229..35046278
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    33429010..33429059
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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