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LOC130060440 ATAC-STARR-seq lymphoblastoid silent region 8282 [ Homo sapiens (human) ]

Gene ID: 130060440, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130060440
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8282
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 LOC130060440 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (19004636..19004935)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (18951142..18951441)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene phosphoribosyl pyrophosphate synthetase associated protein 2 Neighboring gene RAN binding protein 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11846 Neighboring gene small nucleolar RNA MBII-202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18850561-18851174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18851175-18851788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18864393-18865390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18866439-18866973 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18866974-18867507 Neighboring gene solute carrier family 5 member 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18871247-18872190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18874077-18875018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18883844-18884799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18884800-18885754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18885755-18886709 Neighboring gene family with sequence similarity 83 member G Neighboring gene Sharpr-MPRA regulatory region 2479 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18917397-18918386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11848 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18934086-18934883 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18935718-18936468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18936469-18937218 Neighboring gene GRB2 related adaptor protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18954567-18955068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18955069-18955568 Neighboring gene small nucleolar RNA, C/D box 3B-1

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

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_195757.1 

    Range
    101..400
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    19004636..19004935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    18951142..18951441
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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