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LOC130004644 ATAC-STARR-seq lymphoblastoid silent region 2785 [ Homo sapiens (human) ]

Gene ID: 130004644, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004644
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2785
Gene type
biological region
Feature type(s)
regulatory: silencer
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 a silencer based on its ability to repress 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 LOC130004644 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (103584414..103584473)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (104471731..104471790)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (105344171..105344230)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene NEURL1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105253807-105254356 Neighboring gene Sharpr-MPRA regulatory region 14515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3966 Neighboring gene neuralized E3 ubiquitin protein ligase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105287340-105287840 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105287841-105288341 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105323539-105324519 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105329056-105329556 Neighboring gene uncharacterized LOC124902496 Neighboring gene Sharpr-MPRA regulatory region 3797 Neighboring gene Sharpr-MPRA regulatory region 15000 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105367121-105367978 Neighboring gene SH3 and PX domains 2A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105380856-105381356 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105395283-105395862 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105396445-105397024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105399548-105400343 Neighboring gene Sharpr-MPRA regulatory region 2777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105417537-105418038 Neighboring gene uncharacterized LOC124902495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105441739-105442519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105451952-105452918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105455468-105456214 Neighboring gene NFE2L2 motif-containing MPRA enhancer 292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105467435-105468414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105468415-105469393 Neighboring gene NANOG hESC enhancer GRCh37_chr10:105482339-105482840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105491951-105492499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105492500-105493047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105505582-105506103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105506520-105507020 Neighboring gene SH3PXD2A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105507021-105507521

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_184089.1 

    Range
    101..160
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    103584414..103584473
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    104471731..104471790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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