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LOC130002914 ATAC-STARR-seq lymphoblastoid active region 29242 [ Homo sapiens (human) ]

Gene ID: 130002914, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002914
Gene description
ATAC-STARR-seq lymphoblastoid active region 29242
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 LOC130002914 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (133463170..133463229)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (145677614..145677673)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (136328292..136328351)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene surfeit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20456 Neighboring gene serine/threonine kinase like domain containing 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:136257045-136257682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136265498-136266135 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136267839-136268006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136269742-136270242 Neighboring gene REX4 homolog, 3'-5' exonuclease Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29238 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20458 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136295843-136296052 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136321575-136321727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136322178-136323045 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136327558-136328114 Neighboring gene uncharacterized LOC124902295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20462 Neighboring gene calcium channel flower domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136344231-136344732 Neighboring gene solute carrier family 2 member 6

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_182360.1 

    Range
    101..160
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    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    133463170..133463229
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646201.1 Reference GRCh38.p14 PATCHES

    Range
    289264..289323
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    145677614..145677673
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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