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LOC130061860 ATAC-STARR-seq lymphoblastoid silent region 9072 [ Homo sapiens (human) ]

Gene ID: 130061860, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061860
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9072
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 LOC130061860 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 (78782053..78782332)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (79676853..79677132)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (76778135..76778414)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904066 Neighboring gene MPRA-validated peak3019 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76662364-76662975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76662976-76663586 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76663587-76664197 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76664198-76664807 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76671141-76672019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76672283-76672784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76672785-76673284 Neighboring gene cytohesin 1 Neighboring gene RNA, U6 small nuclear 638, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76719667-76720172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12905 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12909 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76770651-76771152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9073 Neighboring gene CRISPRi-validated cis-regulatory element chr17.5512 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47538 Neighboring gene ubiquitin specific peptidase 36 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76834350-76834864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76834865-76835379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12913 Neighboring gene uncharacterized LOC124904067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9075 Neighboring gene ribosomal protein L9 pseudogene 29

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_196966.1 

    Range
    101..380
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    78782053..78782332
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    79676853..79677132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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