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LOC129929627 ATAC-STARR-seq lymphoblastoid silent region 390 [ Homo sapiens (human) ]

Gene ID: 129929627, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129929627
Gene description
ATAC-STARR-seq lymphoblastoid silent region 390
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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Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (21814630..21814749)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (21638573..21638692)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr1:21928741-21928970 Neighboring gene Sharpr-MPRA regulatory region 12165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21937517-21938264 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:21939576-21939868 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21945135-21945976 Neighboring gene RAP1 GTPase activating protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21958265-21959233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21960338-21961086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21961087-21961835 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21966135-21966964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21977615-21978365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 385 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21992551-21993051 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 387 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:21996570-21997769 Neighboring gene ubiquitin specific peptidase 48 Neighboring gene uncharacterized LOC124904736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 336 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:22099067-22099566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 337 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22108688-22109459 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22109460-22110230 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22112153-22112327 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22137244-22137394 Neighboring gene Sharpr-MPRA regulatory region 6146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22148116-22148982 Neighboring gene low density lipoprotein receptor class A domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22168222-22168722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22170194-22170694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22174882-22175382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22175383-22175883 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:22178409-22179608 Neighboring gene heparan sulfate proteoglycan 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22191053-22191858 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22191859-22192664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 341 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22235910-22236626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22236627-22237342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22237343-22238058 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22241885-22242040 Neighboring gene Sharpr-MPRA regulatory region 4422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22246290-22246830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22247372-22247912 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22248108-22248275 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22248994-22249533 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22254196-22254752 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22254753-22255307 Neighboring gene ribosomal protein L21 pseudogene 29 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22258036-22258798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22262253-22263094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22271072-22271789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22288389-22289052 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22290537-22290804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22312621-22313122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22313123-22313622 Neighboring gene RNA, 7SL, cytoplasmic 386, pseudogene Neighboring gene chymotrypsin like elastase 3B

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

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_162684.1 

    Range
    101..220
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    21814630..21814749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    21638573..21638692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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