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LOC130059731 ATAC-STARR-seq lymphoblastoid silent region 7857 [ Homo sapiens (human) ]

Gene ID: 130059731, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059731
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7857
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 LOC130059731 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (88570094..88570423)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (94637700..94638029)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (88636502..88636831)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein, FOG family member 1 Neighboring gene ZFPM1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88591868-88592455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88592456-88593042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88593270-88594010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88594011-88594750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88599832-88600392 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:88600393-88600954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88606102-88606704 Neighboring gene ZC3H18 antisense RNA 1 (head to head) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11355 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11356 Neighboring gene zinc finger CCCH-type containing 18 Neighboring gene Sharpr-MPRA regulatory region 13594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11357 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:88673559-88674059 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88676553-88677498 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88694002-88694718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88694719-88695433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88701182-88702111 Neighboring gene uncharacterized LOC124903755 Neighboring gene interleukin 17C

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_194152.1 

    Range
    101..430
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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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    88570094..88570423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    94637700..94638029
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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