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LOC129929322 ATAC-STARR-seq lymphoblastoid silent region 215 [ Homo sapiens (human) ]

Gene ID: 129929322, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929322
Gene description
ATAC-STARR-seq lymphoblastoid silent region 215
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 LOC129929322 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 (9183086..9183195)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (8717714..8717823)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (9243145..9243254)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9164158-9165134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 114 Neighboring gene MPRA-validated peak53 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9181680-9182180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9182181-9182681 Neighboring gene G protein-coupled receptor 157 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9196849-9197350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9197351-9197850 Neighboring gene Sharpr-MPRA regulatory region 7425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 118 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:9211645-9211881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 210 Neighboring gene MIR34A host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9229591-9230092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9230093-9230592 Neighboring gene microRNA 34a Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9240951-9241812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9241813-9242673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 214 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9243535-9244395 Neighboring gene long non coding transcriptional activator of miR34a Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9258086-9258606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9275966-9276493 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9300874-9301539 Neighboring gene uncharacterized LOC124903836 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9308569-9309492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9309493-9310416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9311341-9312263 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:9312526-9313085 Neighboring gene hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_9566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9364927-9365774 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:9376867-9377040 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:9377645-9378844 Neighboring gene splA/ryanodine receptor domain and SOCS box containing 1 Neighboring gene Sharpr-MPRA regulatory region 3390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9410201-9410702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9410703-9411202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9412777-9413692

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_162379.1 

    Range
    101..210
    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
    9183086..9183195
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    8717714..8717823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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