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LOC130061287 ATAC-STARR-seq lymphoblastoid active region 12471 [ Homo sapiens (human) ]

Gene ID: 130061287, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061287
Gene description
ATAC-STARR-seq lymphoblastoid active region 12471
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC130061287 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 (58334248..58334297)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (59202128..59202177)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (56411609..56411658)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:56379736-56380356 Neighboring gene Sharpr-MPRA regulatory region 10051 Neighboring gene TSPO associated protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56386896-56387595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56389497-56390115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8762 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56402416-56402964 Neighboring gene TSPOAP1, SUPT4H1 and RNF43 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12470 Neighboring gene MIR142 host genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56412683-56413183 Neighboring gene microRNA 142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:56413329-56413870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12477 Neighboring gene Sharpr-MPRA regulatory regions 8228 and 8679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12479 Neighboring gene microRNA 4736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12481 Neighboring gene SPT4 homolog, DSIF elongation factor subunit Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8768

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_196475.1 

    Range
    101..150
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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
    58334248..58334297
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    59202128..59202177
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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