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LOC130060353 ATAC-STARR-seq lymphoblastoid active region 11780 [ Homo sapiens (human) ]

Gene ID: 130060353, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060353
Gene description
ATAC-STARR-seq lymphoblastoid active region 11780
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 LOC130060353 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 (16981267..16981476)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (16927343..16927552)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (16884581..16884790)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:16828359-16829044 Neighboring gene TBC1 domain family member 27, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11773 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16840494-16840994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16841792-16842632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16846756-16847256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16847257-16847757 Neighboring gene TNF receptor superfamily member 13B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16847819-16848342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16848867-16849390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16849391-16849914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11779 Neighboring gene uncharacterized LOC284191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16884947-16885486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16885487-16886025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16890303-16891133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11784 Neighboring gene long intergenic non-protein coding RNA 2090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16899244-16899806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11785 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16908048-16908576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16914402-16915394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16923086-16924033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16932678-16933252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11786 Neighboring gene uncharacterized LOC124903938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8233

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_194774.1 

    Range
    101..310
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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
    16981267..16981476
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    16927343..16927552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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