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LOC130003146 ATAC-STARR-seq lymphoblastoid active region 29367 [ Homo sapiens (human) ]

Gene ID: 130003146, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003146
Gene description
ATAC-STARR-seq lymphoblastoid active region 29367
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 LOC130003146 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 (137761223..137761372)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (150018788..150018937)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140655675..140655824)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene euchromatic histone lysine methyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29357 Neighboring gene SET pseudogene 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140558803-140559307 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140559363-140560044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140569123-140569639 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:140573165-140573881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140574605-140575206 Neighboring gene uncharacterized LOC124902319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140575207-140575806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140576860-140577836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140584357-140584859 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140589985-140590669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140602949-140603910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20637 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140616633-140617551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140617552-140618469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140621001-140621500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29361 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140635595-140636095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140643003-140643502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140652245-140652746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29369 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:140657628-140658827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140674415-140675346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140676414-140676914 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:140679830-140680474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140681121-140681765 Neighboring gene forkhead box H1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140682311-140682830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140682831-140683350 Neighboring gene uncharacterized LOC651337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29371 Neighboring gene microRNA 602

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_182592.1 

    Range
    101..250
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    137761223..137761372
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    150018788..150018937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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