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LOC130060356 ATAC-STARR-seq lymphoblastoid active region 11785 [ Homo sapiens (human) ]

Gene ID: 130060356, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060356
Gene description
ATAC-STARR-seq lymphoblastoid active region 11785
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 LOC130060356 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 (16997538..16997587)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (16943619..16943668)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (16900852..16900901)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes 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 ATAC-STARR-seq lymphoblastoid active region 11780 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 uncharacterized LOC284191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16890303-16891133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16899244-16899806 Neighboring gene long intergenic non-protein coding RNA 2090 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 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:16946458-16947657 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16959278-16959917 Neighboring gene myosin phosphatase Rho interacting protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16975468-16975993 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16975994-16976520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16991083-16991584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16999002-16999588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17011600-17012124 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17022544-17023069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17029831-17030330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17030795-17031296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17031297-17031796 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17034927-17035431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11788 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17043984-17044574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17045275-17045817 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17045818-17046359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17070554-17071156 Neighboring gene RNA, U6 small nuclear 767, pseudogene

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_194777.1 

    Range
    101..150
    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
    16997538..16997587
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    16943619..16943668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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