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LOC130001279 ATAC-STARR-seq lymphoblastoid active region 28042 [ Homo sapiens (human) ]

Gene ID: 130001279, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001279
Gene description
ATAC-STARR-seq lymphoblastoid active region 28042
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 LOC130001279 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (141106614..141106953)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (142226737..142227076)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (142116713..142117052)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142047320-142047944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142047945-142048570 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142048571-142049195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142051549-142052338 Neighboring gene uncharacterized LOC105375784 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142069799-142070496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:142077205-142077706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142082933-142083432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142083433-142084432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142084444-142085234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142085235-142086025 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19587 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142097256-142097756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28041 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:142104647-142104880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142105126-142106125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142114470-142115018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142115019-142115566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142121985-142122506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142122507-142123026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142128597-142129165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142137284-142138115 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142138949-142139779 Neighboring gene DENND3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:142144757-142145375 Neighboring gene DENN domain containing 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142163840-142164798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142167099-142167874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28046 Neighboring gene Sharpr-MPRA regulatory region 5779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142183015-142183516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142183517-142184016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142191187-142191687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28049 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28051 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142194501-142195455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142202224-142202724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142202725-142203225 Neighboring gene uncharacterized LOC105375785

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_180725.1 

    Range
    101..440
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    141106614..141106953
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    142226737..142227076
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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