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LOC129991998 ATAC-STARR-seq lymphoblastoid silent region 15136 [ Homo sapiens (human) ]

Gene ID: 129991998, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129991998
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15136
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 LOC129991998 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (1683719..1683818)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (1681596..1681695)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (1685446..1685545)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374348 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1513782-1514432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1522059-1522612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1545561-1546304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1546305-1547046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1550615-1551471 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1553567-1553737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1562577-1563106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1568111-1568928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1568929-1569747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1569748-1570565 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:1573296-1574073 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:1574074-1574850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1577987-1578860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1578861-1579734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1579735-1580607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15134 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1582889-1583115 Neighboring gene family with sequence similarity 53 member A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1595837-1596352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1600440-1601266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1605640-1606631 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1606632-1607622 Neighboring gene VISTA enhancer hs526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1616583-1617084 Neighboring gene uncharacterized LOC105374349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1648945-1649446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15137 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1686561-1687180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1687181-1687800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1707982-1708482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21158 Neighboring gene stem-loop histone mRNA binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1723083-1724078 Neighboring gene transmembrane protein 129, E3 ubiquitin ligase

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_171444.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    1683719..1683818
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    1681596..1681695
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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