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LOC130004974 ATAC-STARR-seq lymphoblastoid silent region 2945 [ Homo sapiens (human) ]

Gene ID: 130004974, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130004974
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2945
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 LOC130004974 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (131668972..131669021)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (132602928..132602977)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene transcription elongation regulator 1 like Neighboring gene uncharacterized LOC105378563 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133048467-133049038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133047894-133048466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133049039-133049610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133050816-133051316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133051317-133051817 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133057495-133058060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133060331-133060830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133062787-133063287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133075620-133076135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133077535-133078178 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:133078179-133078822 Neighboring gene uncharacterized LOC101927461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133118937-133119655 Neighboring gene OCT4 hESC enhancer GRCh37_chr10:133148496-133148998 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:133187995-133188149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133200719-133201394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133224627-133225606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133239161-133239678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133252429-133252973 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133312838-133313402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133314802-133315328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133327982-133328482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133329536-133330299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133344133-133344690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133344691-133345247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133378011-133378511 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133379432-133379970 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:133467536-133468735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133469096-133469596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133469597-133470097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133478856-133479820 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:133479821-133480784 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:133483756-133484448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4218 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133509356-133509977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133509978-133510600 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133510601-133511221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133513041-133513838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133513839-133514635 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133517485-133517986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133517987-133518486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133520926-133521590 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133521591-133522253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133527621-133528122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133532727-133533402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133534466-133535216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133535217-133535966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4219 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:133584321-133585520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133588432-133588932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133588933-133589433 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133602465-133602964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133605578-133606078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133606079-133606579 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:133609642-133610841 Neighboring gene long intergenic non-protein coding RNA 1164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133638117-133638714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133638715-133639311 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133655059-133656046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133656047-133657034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133657035-133658020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133673472-133674089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133674090-133674706 Neighboring gene uncharacterized LOC105378565

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

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_184419.1 

    Range
    101..150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    131668972..131669021
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    132602928..132602977
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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