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LOC129998600 ATAC-STARR-seq lymphoblastoid silent region 18258 [ Homo sapiens (human) ]

Gene ID: 129998600, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998600
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18258
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 LOC129998600 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 (73667502..73667601)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (74868417..74868516)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (73081832..73081931)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26125 Neighboring gene transducin beta like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73001900-73002400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73002401-73002901 Neighboring gene Sharpr-MPRA regulatory region 5103 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73017160-73017696 Neighboring gene MLX interacting protein like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73021869-73022452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73049903-73050752 Neighboring gene Sharpr-MPRA regulatory region 8994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18259 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73082323-73083318 Neighboring gene VPS37D subunit of ESCRT-I Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26127 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73098635-73099484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73099485-73100334 Neighboring gene DnaJ heat shock protein family (Hsp40) member C30 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:73104307-73104476 Neighboring gene BUD23 rRNA methyltransferase and ribosome maturation 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_178046.1 

    Range
    101..200
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    73667502..73667601
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    74868417..74868516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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