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LOC130060404 ATAC-STARR-seq lymphoblastoid active region 11816 [ Homo sapiens (human) ]

Gene ID: 130060404, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130060404
Gene description
ATAC-STARR-seq lymphoblastoid active region 11816
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 LOC130060404 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 (17890951..17891100)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17837638..17837787)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17722069-17722789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11811 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:17726733-17726883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11813 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17730461-17731182 Neighboring gene microRNA 6777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17731183-17731904 Neighboring gene sterol regulatory element binding transcription factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17733682-17734430 Neighboring gene microRNA 33b Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17734431-17735178 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17739175-17740076 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17740077-17740979 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17740980-17741881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17743523-17744042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17745179-17745680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17747581-17748101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17751860-17752706 Neighboring gene Sharpr-MPRA regulatory region 7387 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17762139-17762639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11815 Neighboring gene target of myb1 like 2 membrane trafficking protein Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:17779053-17780252 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17780613-17781334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17787373-17788134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17788135-17788894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17792123-17792624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17817644-17818266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17823655-17824188 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17824189-17824722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17825257-17825790 Neighboring gene Sharpr-MPRA regulatory region 12990 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17825791-17826324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17826325-17826857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17875207-17875776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11819 Neighboring gene uncharacterized LOC107984989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17884370-17884870 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:17898150-17898316 Neighboring gene dynein regulatory complex subunit 3 Neighboring gene brain protein I3 pseudogene 3 Neighboring gene ribosomal protein S2 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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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_194792.1 

    Range
    101..250
    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
    17890951..17891100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    17837638..17837787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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