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LOC129936563 ATAC-STARR-seq lymphoblastoid active region 19746 [ Homo sapiens (human) ]

Gene ID: 129936563, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936563
Gene description
ATAC-STARR-seq lymphoblastoid active region 19746
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 LOC129936563 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 (42582253..42582382)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (42600247..42600376)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (42623745..42623874)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42542633-42543206 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14244 Neighboring gene Sharpr-MPRA regulatory region 5178 Neighboring gene vasoactive intestinal peptide receptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:42566136-42566306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42574871-42575372 Neighboring gene VIPR1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42581415-42581916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42581917-42582416 Neighboring gene SEC22 homolog C, vesicle trafficking protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:42622926-42623752 Neighboring gene SS18 like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14246 Neighboring gene ZBTB47 and NKTR antisense RNA 1 Neighboring gene natural killer cell triggering receptor Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:42672544-42673392 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:42673393-42674241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42695163-42695804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14248 Neighboring gene Sharpr-MPRA regulatory region 3469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42700825-42701735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42701736-42702645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19749 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42706502-42707002 Neighboring gene uncharacterized LOC124906232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42708562-42709098 Neighboring gene zinc finger and BTB domain containing 47

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 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_169574.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    42582253..42582382
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    42600247..42600376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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