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LOC130067195 ATAC-STARR-seq lymphoblastoid silent region 13603 [ Homo sapiens (human) ]

Gene ID: 130067195, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130067195
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13603
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 LOC130067195 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (30255915..30256034)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30719233..30719352)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30637625-30638293 Neighboring gene LIF antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30640698-30641198 Neighboring gene LIF interleukin 6 family cytokine Neighboring gene LIF antisense RNA 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30648163-30648928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30648929-30649693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30650183-30650684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30650685-30651184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30653067-30653669 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30653670-30654271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30656529-30657028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30659020-30659819 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30659820-30660618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18830 Neighboring gene oncostatin M Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30672215-30672804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30673676-30674204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30674205-30674733 Neighboring gene cytosolic arginine sensor for mTORC1 subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13605

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_201610.1 

    Range
    101..220
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    30255915..30256034
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    30719233..30719352
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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