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LOC130004007 ATAC-STARR-seq lymphoblastoid silent region 2446 [ Homo sapiens (human) ]

Gene ID: 130004007, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004007
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2446
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 LOC130004007 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 (70404017..70404206)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (71273074..71273263)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (72163773..72163962)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene leucine rich repeat containing 20 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2444 Neighboring gene Sharpr-MPRA regulatory region 4423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72094756-72095256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3502 Neighboring gene NANOG hESC enhancer GRCh37_chr10:72128656-72129157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72141592-72142211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3504 Neighboring gene centrosomal protein 57 like 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2447 Neighboring gene eukaryotic translation initiation factor 4E binding protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72194899-72195400 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72197102-72197282 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72199683-72200292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72200293-72200900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72200901-72201510 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72202121-72202730 Neighboring gene Sharpr-MPRA regulatory region 10829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72210316-72210984 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:72214954-72215480 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72215481-72216006 Neighboring gene nodal growth differentiation factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72232724-72233490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72239853-72240495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72240496-72241137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72242631-72243178 Neighboring gene phosphatase domain containing paladin 1 Neighboring gene YY1 transcription factor pseudogene 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 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_183453.1 

    Range
    101..290
    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
    70404017..70404206
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    71273074..71273263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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