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LOC129998956 ATAC-STARR-seq lymphoblastoid silent region 18444 [ Homo sapiens (human) ]

Gene ID: 129998956, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998956
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18444
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 LOC129998956 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 (100570079..100570278)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101810161..101810360)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100167702..100167901)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 416, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr7.3530 Neighboring gene NANOG hESC enhancer GRCh37_chr7:100136176-100136677 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18443 Neighboring gene uncharacterized LOC124901708 Neighboring gene ArfGAP with FG repeats 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100166771-100167442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100168785-100169455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100172387-100172941 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100172942-100173495 Neighboring gene insulin receptor substrate 3, pseudogene Neighboring gene Sin3A associated protein 25 Neighboring gene leucine rich repeats and calponin homology domain containing 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100181227-100181915 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100182061-100182574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100182575-100183088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18446

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_178401.1 

    Range
    101..300
    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
    100570079..100570278
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    101810161..101810360
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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