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LOC129998993 ATAC-STARR-seq lymphoblastoid active region 26395 [ Homo sapiens (human) ]

Gene ID: 129998993, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998993
Gene description
ATAC-STARR-seq lymphoblastoid active region 26395
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 LOC129998993 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 (101017372..101017421)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102340108..102340157)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100660653..100660702)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375431 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:100541229-100541778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100546705-100547685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100547686-100548665 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:100548721-100549266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:100551103-100551603 Neighboring gene uncharacterized LOC124900622 Neighboring gene mucin 3A, cell surface associated Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18473 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18472 Neighboring gene mucin 12, cell surface associated Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:100640603-100641456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100641457-100642309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100658552-100659220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26396 Neighboring gene Sharpr-MPRA regulatory region 8701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26397 Neighboring gene MUC12 antisense RNA 1 Neighboring gene mucin 17, cell surface associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100709117-100709986 Neighboring gene RN7SK pseudogene 54 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:100727119-100727619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100730454-100731094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100731095-100731734 Neighboring gene tripartite motif containing 56

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_178438.1 

    Range
    101..150
    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
    101017372..101017421
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    102340108..102340157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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