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LOC130057517 ATAC-STARR-seq lymphoblastoid active region 9748 [ Homo sapiens (human) ]

Gene ID: 130057517, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057517
Gene description
ATAC-STARR-seq lymphoblastoid active region 9748
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 LOC130057517 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (74374136..74374185)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72241864..72241913)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74666477..74666526)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene cytochrome P450 family 11 subfamily A member 1 Neighboring gene uncharacterized LOC124903524 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6646 Neighboring gene CYP11A1 promoter region Neighboring gene peptidylprolyl isomerase A pseudogene 46 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6647 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74667008-74667555 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9749 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74670820-74671320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9751 Neighboring gene long intergenic non-protein coding RNA 2255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74675326-74675826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9753 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:74676645-74677844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74678372-74678912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74678913-74679452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74679453-74679994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74679995-74680534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74680535-74681075 Neighboring gene CRISPRi-validated cis-regulatory element chr15.2230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9758 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:74688843-74690042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74692014-74692514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74693783-74694283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74695428-74696393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74701581-74702081 Neighboring gene semaphorin 7A (JohnMiltonHagen blood group) Neighboring gene microRNA 6881

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_191938.1 

    Range
    101..150
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    74374136..74374185
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160016.1 Reference GRCh38.p14 PATCHES

    Range
    203405..203454
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    72241864..72241913
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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