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LOC129936175 ATAC-STARR-seq lymphoblastoid active region 19445 [ Homo sapiens (human) ]

Gene ID: 129936175, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936175
Gene description
ATAC-STARR-seq lymphoblastoid active region 19445
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 LOC129936175 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (12560772..12560951)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (12558576..12558755)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (12602271..12602450)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene tRNA splicing endonuclease subunit 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12558643-12559143 Neighboring gene RNA, 5S ribosomal pseudogene 123 Neighboring gene RNA, U6 small nuclear 377, pseudogene Neighboring gene MKRN2 opposite strand Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14065 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12598813-12599336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19446 Neighboring gene makorin ring finger protein 2 Neighboring gene MPRA-validated peak4543 silencer Neighboring gene Raf-1 proto-oncogene, serine/threonine kinase Neighboring gene small nucleolar RNA U13 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:12684584-12684794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12698025-12698668 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12704698-12705308 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12705309-12705920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19449 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12711892-12712473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12712474-12713054 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12715375-12716244 Neighboring gene cysteine rich protein 1 pseudogene 1

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_169186.1 

    Range
    101..280
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    12560772..12560951
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    12558576..12558755
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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