U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129936927 ATAC-STARR-seq lymphoblastoid active region 19986 [ Homo sapiens (human) ]

Gene ID: 129936927, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129936927
Gene description
ATAC-STARR-seq lymphoblastoid active region 19986
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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC129936927 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 (57235062..57235201)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (57275330..57275469)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (57269090..57269229)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene interleukin 17 receptor D Neighboring gene uncharacterized LOC105377101 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:57192947-57193632 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:57193633-57194316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14479 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:57218732-57218927 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:57233699-57234296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14480 Neighboring gene HESX homeobox 1 Neighboring gene uncharacterized LOC105377102 Neighboring gene adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1 Neighboring gene MPRA-validated peak4664 silencer Neighboring gene uncharacterized LOC124909384 Neighboring gene ankyrin repeat and SOCS box containing 14 Neighboring gene dynein axonemal heavy chain 12

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_169938.1 

    Range
    101..240
    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
    57235062..57235201
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    57275330..57275469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases