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LOC129935925 ATAC-STARR-seq lymphoblastoid silent region 12481 [ Homo sapiens (human) ]

Gene ID: 129935925, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935925
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12481
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 LOC129935925 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (237698357..237698406)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (238188356..238188405)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (238607000..238607049)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238503899-238504617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238504725-238505226 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238512736-238513239 Neighboring gene RAB17 divergent transcript Neighboring gene VISTA enhancer hs1945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238539637-238540136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238540139-238540700 Neighboring gene LRR binding FLII interacting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238558724-238559224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238559225-238559725 Neighboring gene NANOG hESC enhancer GRCh37_chr2:238571326-238571867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238572854-238573422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238581723-238582348 Neighboring gene Sharpr-MPRA regulatory region 636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238583717-238584263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238595001-238595502 Neighboring gene uncharacterized LOC124906128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238595503-238596002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238599723-238600598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238611455-238612335 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238612336-238613215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238626179-238626695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238630967-238631468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238631469-238631968 Neighboring gene Sharpr-MPRA regulatory region 7631 Neighboring gene Sharpr-MPRA regulatory region 7730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238653055-238653580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17376 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:238671072-238671284 Neighboring gene RNA binding motif protein 44 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238766078-238766866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238766867-238767653 Neighboring gene small nucleolar RNA SNORD55/SNORD39 Neighboring gene receptor activity modifying protein 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_168936.1 

    Range
    101..150
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    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    237698357..237698406
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    238188356..238188405
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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