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LOC129999746 ATAC-STARR-seq lymphoblastoid active region 26923 [ Homo sapiens (human) ]

Gene ID: 129999746, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999746
Gene description
ATAC-STARR-seq lymphoblastoid active region 26923
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 LOC129999746 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (157302331..157302460)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (158490159..158490288)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (157095025..157095154)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ubiquitin protein ligase E3C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157064509-157065277 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157065278-157066047 Neighboring gene ribosomal protein L36a pseudogene 30 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157074692-157075645 Neighboring gene uncharacterized LOC124901803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157081913-157082520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157082521-157083126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157084407-157085020 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:157092843-157093017 Neighboring gene Sharpr-MPRA regulatory region 5233 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26924 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157100891-157101432 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157101433-157101972 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157101973-157102514 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr7:157102515-157103054 and GRCh37_chr7:157103055-157103596 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157103597-157104136 Neighboring gene Sharpr-MPRA regulatory region 5385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157129649-157130152 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157129146-157129648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157133233-157133753 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157141921-157142490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26928 Neighboring gene DnaJ heat shock protein family (Hsp40) member B6 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:157166121-157166319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157182939-157183539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157193377-157193935 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157194192-157195182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157198555-157199224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157201081-157202080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157202081-157203080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157203081-157204078 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:157220516-157220681 Neighboring gene MPRA-validated peak6870 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157225071-157225580 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:157234065-157234596 Neighboring gene uncharacterized LOC101927914 Neighboring gene Sharpr-MPRA regulatory region 4962 Neighboring gene MPRA-validated peak6872 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26930

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_179192.1 

    Range
    101..230
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    157302331..157302460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    158490159..158490288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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