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LOC129994700 ATAC-STARR-seq lymphoblastoid active region 23173 [ Homo sapiens (human) ]

Gene ID: 129994700, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994700
Gene description
ATAC-STARR-seq lymphoblastoid active region 23173
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 LOC129994700 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (135456414..135456463)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (135983585..135983634)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (134792104..134792153)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PITX1 antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:134678129-134679328 Neighboring gene macroH2A.1 histone Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16373 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16375 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:134735167-134735672 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:134735673-134736178 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:134739095-134739661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23171 Neighboring gene VISTA enhancer hs1473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134784907-134785408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134785409-134785908 Neighboring gene uncharacterized LOC124901073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23175 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:134820245-134821093 Neighboring gene dendritic cell associated nuclear protein 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134824474-134825331 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134825332-134826188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134826189-134827045 Neighboring gene TIFA inhibitor Neighboring gene MPRA-validated peak5480 silencer Neighboring gene Sharpr-MPRA regulatory region 242 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134871641-134872156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134877514-134878015 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134878708-134879599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134879600-134880490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134880491-134881382 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:134900858-134901378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134904009-134904938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134905671-134906171 Neighboring gene neurogenin 1 Neighboring gene C-X-C motif chemokine ligand 14

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_174146.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    135456414..135456463
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    135983585..135983634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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