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LOC129997630 ATAC-STARR-seq lymphoblastoid active region 25409 [ Homo sapiens (human) ]

Gene ID: 129997630, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997630
Gene description
ATAC-STARR-seq lymphoblastoid active region 25409
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 LOC129997630 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 (161029412..161029511)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (162387824..162387923)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (161450444..161450543)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378093 Neighboring gene uncharacterized LOC102724087 Neighboring gene Sharpr-MPRA regulatory region 6130 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:161396855-161397569 Neighboring gene MPRA-validated peak6299 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25407 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:161412339-161413208 Neighboring gene Sharpr-MPRA regulatory region 85 Neighboring gene MAP3K4 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr6:161422459-161422960 Neighboring gene mitogen-activated protein kinase kinase kinase 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25410 Neighboring gene MPRA-validated peak6300 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:161500530-161501729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25411 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:161549261-161550460 Neighboring gene Sharpr-MPRA regulatory region 15502 Neighboring gene uncharacterized LOC124901455 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:161579309-161579810 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:161579811-161580310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:161581716-161582274 Neighboring gene 1-acylglycerol-3-phosphate O-acyltransferase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:161582962-161583462 Neighboring gene AGPAT4 intronic transcript 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_177076.1 

    Range
    101..200
    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
    161029412..161029511
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    162387824..162387923
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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