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LOC129992161 ATAC-STARR-seq lymphoblastoid silent region 15227 [ Homo sapiens (human) ]

Gene ID: 129992161, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129992161
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15227
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 LOC129992161 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (6200205..6200964)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (6174161..6174920)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (6201932..6202691)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5926351-5926851 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5932940-5933440 Neighboring gene chromosome 4 open reading frame 50 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5947182-5947682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:5957977-5958528 Neighboring gene microRNA 378d-1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5972715-5973525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5975147-5975708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5975709-5976269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5995614-5996166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5996167-5996718 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:6050907-6052106 Neighboring gene uncharacterized LOC128125818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6071730-6072660 Neighboring gene janus kinase and microtubule interacting protein 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6073591-6074520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6087461-6088334 Neighboring gene NANOG hESC enhancer GRCh37_chr4:6089664-6090166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6093535-6094036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6107415-6107947 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6118271-6118786 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:6118787-6119302 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6119819-6120334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6142439-6142940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6192917-6193537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21258 Neighboring gene JAKMIP1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6247680-6248310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6264593-6265371 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:6266160-6267359 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6274585-6275134 Neighboring gene VISTA enhancer hs1979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6333689-6334190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6340800-6341378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6341379-6341956 Neighboring gene wolframin ER transmembrane glycoprotein Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:6369538-6370278 Neighboring gene protein phosphatase 2 regulatory subunit Bgamma Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:6368797-6369537 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6371026-6371745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6378434-6379114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6390823-6391322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6392177-6392889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6394915-6395468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6395469-6396022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6445131-6445630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6464699-6465244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6465245-6465790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6471820-6472650 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6528063-6528950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6528951-6529838 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6529839-6530726 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:6530727-6531613 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6551456-6551956 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:6551957-6552457

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_171607.1 

    Range
    101..860
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    6200205..6200964
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    6174161..6174920
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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