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LOC130006301 ATAC-STARR-seq lymphoblastoid silent region 3704 [ Homo sapiens (human) ]

Gene ID: 130006301, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006301
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3704
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 LOC130006301 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (70399386..70399455)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (70419808..70419877)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (70245492..70245561)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369373 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:70175478-70175614 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70187532-70188110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70188111-70188688 Neighboring gene PTPRF interacting protein alpha 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70230466-70230972 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:70235067-70235838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70235839-70236608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70237380-70238149 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:70242965-70243153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3703 Neighboring gene Sharpr-MPRA regulatory region 1776 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:70250285-70250464 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:70261331-70261532 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:70265651-70266850 Neighboring gene CTTN divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70289993-70290826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70343973-70344473 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:70346781-70346940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70351607-70352106 Neighboring gene cortactin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70364325-70364826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70369495-70370452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70370453-70371408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70371409-70372366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70373323-70374279 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70384621-70385240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70385241-70385858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70390839-70391673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70392509-70393343 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70393780-70394730 Neighboring gene SH3 and multiple ankyrin repeat domains 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70397475-70397990 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:70399135-70400334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70404151-70404881 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70403420-70404150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70422686-70423186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70423187-70423687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70425215-70425716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70428716-70429218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70429219-70429720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70429721-70430223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70430775-70431315 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70457727-70458490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70464553-70465368 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70465369-70466183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70483308-70484149 Neighboring gene Sharpr-MPRA regulatory region 3810 Neighboring gene SHANK2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70508534-70509208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70509209-70509883 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70516085-70516612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70519247-70519774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70526489-70527252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70527253-70528017 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70533609-70534130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70534131-70534652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70555908-70556529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70559535-70560424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70560938-70561770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70563993-70564502 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:70565347-70565550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70585495-70586046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70586047-70586598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70591157-70591852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70591853-70592548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70592549-70593244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70614429-70614930 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:70634290-70635489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70680550-70681124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70681125-70681698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70681699-70682272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70686259-70686758 Neighboring gene SHANK2 antisense RNA 3

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_185746.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    70399386..70399455
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160005.1 Reference GRCh38.p14 PATCHES

    Range
    160674..160743
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    70419808..70419877
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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