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LOC130059955 ATAC-STARR-seq lymphoblastoid silent region 7998 [ Homo sapiens (human) ]

Gene ID: 130059955, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059955
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7998
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 LOC130059955 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (2394167..2394256)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (2282864..2282953)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (2297461..2297550)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7993 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7994 Neighboring gene small nucleolar RNA, C/D box 91A Neighboring gene TSR1 ribosome maturation factor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2251000-2251937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11491 Neighboring gene small G protein signaling modulator 2 Neighboring gene uncharacterized LOC101927864 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2272684-2273268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2273269-2273851 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2273852-2274435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:2289277-2290101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:2291629-2292130 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:2296137-2296704 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:2296705-2297271 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2301897-2302468 Neighboring gene hESC enhancers GRCh37_chr17:2302469-2303038 and GRCh37_chr17:2303039-2303609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11493 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2305321-2305891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:2305892-2306461 Neighboring gene MAX network transcriptional repressor Neighboring gene uncharacterized LOC284009 Neighboring gene methyltransferase 16, RNA N6-adenosine Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2337127-2337806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2337807-2338485 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2338486-2339164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2339165-2339843 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:2383040-2383219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:2398718-2399218 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:2403917-2404418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:2404419-2404918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2409238-2410149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:2410150-2411060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11495

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 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_194376.1 

    Range
    101..190
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    2394167..2394256
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    2282864..2282953
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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