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LOC129997240 ATAC-STARR-seq lymphoblastoid active region 25122 [ Homo sapiens (human) ]

Gene ID: 129997240, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997240
Gene description
ATAC-STARR-seq lymphoblastoid active region 25122
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 LOC129997240 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (136791848..136791917)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (137980029..137980098)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (137112986..137113055)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase kinase kinase 5 Neighboring gene uncharacterized LOC124901410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25121 Neighboring gene Sharpr-MPRA regulatory region 8718 Neighboring gene Sharpr-MPRA regulatory region 14394 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:137112365-137112880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25124 Neighboring gene MAP3K5 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25125 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:137143334-137144066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:137144067-137144799 Neighboring gene MPRA-validated peak6150 silencer Neighboring gene MPRA-validated peak6151 silencer Neighboring gene small nucleolar RNA SNORA27 Neighboring gene peroxisomal biogenesis factor 7 Neighboring gene ribosomal protein L7a pseudogene 37

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_176686.1 

    Range
    101..170
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    136791848..136791917
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    137980029..137980098
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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