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LOC130001774 ATAC-STARR-seq lymphoblastoid active region 28366 [ Homo sapiens (human) ]

Gene ID: 130001774, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001774
Gene description
ATAC-STARR-seq lymphoblastoid active region 28366
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 LOC130001774 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 (36995311..36995380)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (37019018..37019087)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (36995308..36995377)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene paired box 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36867937-36868628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28358 Neighboring gene microRNA 4540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36879416-36880112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36900581-36901081 Neighboring gene microRNA 4476 Neighboring gene MTA1-activated intronic PAX5 enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36947656-36948180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36961379-36962370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36962371-36963361 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36980425-36980924 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:36986501-36987456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36996149-36996649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36997151-36997666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36997667-36998181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28368 Neighboring gene uncharacterized LOC105376032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28371 Neighboring gene Sharpr-MPRA regulatory region 11996 Neighboring gene uncharacterized LOC105376031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37028766-37029440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28373

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_181220.1 

    Range
    101..170
    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
    36995311..36995380
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    37019018..37019087
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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