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LOC130067339 ATAC-STARR-seq lymphoblastoid silent region 13676 [ Homo sapiens (human) ]

Gene ID: 130067339, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067339
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13676
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 LOC130067339 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (37019739..37020058)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (37479338..37479657)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (37415780..37416099)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized protein FLJ39582-like Neighboring gene CRISPRi-validated cis-regulatory element chr22.1656 Neighboring gene CRISPRi-validated cis-regulatory element chr22.1657 Neighboring gene ciliary microtubule inner protein 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37408066-37408566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37408567-37409067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37414031-37415006 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:37415035-37415536 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13675 Neighboring gene thiosulfate sulfurtransferase Neighboring gene mercaptopyruvate sulfurtransferase Neighboring gene uncharacterized LOC112268295 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37428845-37429362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37429455-37430120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37439765-37440678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37447950-37448667 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37448668-37449384 Neighboring gene RN7SK pseudogene 214 Neighboring gene potassium channel tetramerization domain containing 17

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_201754.1 

    Range
    101..420
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    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    37019739..37020058
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    37479338..37479657
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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