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LOC129998158 ATAC-STARR-seq lymphoblastoid silent region 18046 [ Homo sapiens (human) ]

Gene ID: 129998158, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998158
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18046
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 LOC129998158 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (28574060..28574109)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (28711507..28711556)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (28613678..28613727)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene JAZF zinc finger 1 Neighboring gene MPRA-validated peak6455 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25794 Neighboring gene JAZF1 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr7:28330425-28331392 and GRCh37_chr7:28331393-28332360 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:28332361-28333326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:28350942-28351442 Neighboring gene peptidylprolyl isomerase A pseudogene 80 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:28398093-28398687 Neighboring gene cAMP responsive element binding protein 5 Neighboring gene Sharpr-MPRA regulatory region 5389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25797 Neighboring gene Sharpr-MPRA regulatory region 14916 Neighboring gene VISTA enhancer hs1604 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:28651065-28652264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:28682874-28683374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:28683375-28683875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:28725036-28725544 Neighboring gene ribosomal protein S2 pseudogene 30 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25799 Neighboring gene NANOG hESC enhancer GRCh37_chr7:28808272-28808863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:28832834-28833543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25800 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:28877832-28878523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18047 Neighboring gene Sharpr-MPRA regulatory region 6215 Neighboring gene TLR4 interactor with leucine rich repeats

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_177599.1 

    Range
    101..150
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    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    28574060..28574109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    28711507..28711556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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