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LOC129992037 ATAC-STARR-seq lymphoblastoid silent region 15166 [ Homo sapiens (human) ]

Gene ID: 129992037, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129992037
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15166
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 LOC129992037 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 (2418370..2418529)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (2417124..2417283)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (2420097..2420256)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene zinc finger FYVE-type containing 28 Neighboring gene uncharacterized LOC124900649 Neighboring gene uncharacterized LOC105374352 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15165 Neighboring gene uncharacterized LOC107986249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2388710-2389224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2390450-2391184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2391185-2391918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2391919-2392652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2392653-2393385 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:2395333-2395503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21171 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2403273-2403944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2409813-2410318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2413256-2413776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2413777-2414297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2417974-2418532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2418533-2419091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2424482-2425072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2425073-2425662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2425663-2426252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2426253-2426841 Neighboring gene cilia and flagella associated protein 99 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15169 Neighboring gene uncharacterized LOC105374353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2465175-2465674 Neighboring gene uncharacterized LOC107986250

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_171483.1 

    Range
    101..260
    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
    2418370..2418529
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    2417124..2417283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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