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LOC129930208 ATAC-STARR-seq lymphoblastoid silent region 697 [ Homo sapiens (human) ]

Gene ID: 129930208, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129930208
Gene description
ATAC-STARR-seq lymphoblastoid silent region 697
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 LOC129930208 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (39217751..39217800)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (39085158..39085207)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (39683423..39683472)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene microtubule actin crosslinking factor 1 Neighboring gene Sharpr-MPRA regulatory region 301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:39599569-39600336 Neighboring gene RNA, U6 small nuclear 608, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:39605822-39606646 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:39606647-39607470 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:39607555-39608294 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:39637465-39637991 Neighboring gene RNA, 5S ribosomal pseudogene 44 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:39648813-39650012 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:39657180-39657722 Neighboring gene Sharpr-MPRA regulatory region 6545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 806 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:39679473-39680191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 696 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:39691029-39691222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:39698122-39698932 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:39764567-39764723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 810 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 8 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:39811169-39811670 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:39812278-39813477 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:39824023-39825222 Neighboring gene MACF1 eExon liver enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 699 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:39933786-39933926 Neighboring gene uncharacterized LOC124904101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 700

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_163261.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    39217751..39217800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    39085158..39085207
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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