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LOC129935467 ATAC-STARR-seq lymphoblastoid active region 17019 [ Homo sapiens (human) ]

Gene ID: 129935467, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935467
Gene description
ATAC-STARR-seq lymphoblastoid active region 17019
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 LOC129935467 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (205706602..205706741)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (206188942..206189081)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (206571326..206571465)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907967 Neighboring gene par-3 family cell polarity regulator beta Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:205529451-205530018 Neighboring gene uncharacterized LOC124907968 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:205562341-205563540 Neighboring gene NANOG hESC enhancer GRCh37_chr2:205689833-205690426 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:205860967-205861560 Neighboring gene NANOG hESC enhancer GRCh37_chr2:205897477-205897980 Neighboring gene NANOG hESC enhancer GRCh37_chr2:206072806-206073307 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:206078371-206078958 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:206099834-206101033 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:206140682-206141288 Neighboring gene NANOG hESC enhancer GRCh37_chr2:206211338-206211871 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:206543139-206544338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:206549220-206549850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:206560188-206561022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17021 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:206572851-206573627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17020 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:206584967-206585532 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:206585533-206586096 Neighboring gene Sharpr-MPRA regulatory region 14521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:206611361-206611912 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:206612879-206613502 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:206613503-206614126 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:206614127-206614749 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:206617009-206618208 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:206646133-206646356 Neighboring gene NANOG hESC enhancer GRCh37_chr2:206661289-206661790 Neighboring gene uncharacterized LOC105373847 Neighboring gene neuropilin 2 Neighboring gene NANOG hESC enhancer GRCh37_chr2:206700713-206701214 Neighboring gene uncharacterized LOC124907969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:206752118-206752618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:206752619-206753119 Neighboring gene RN7SK pseudogene 178

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_168480.1 

    Range
    101..240
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    205706602..205706741
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    206188942..206189081
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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