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LOC124416876 Sharpr-MPRA regulatory region 3512 [ Homo sapiens (human) ]

Gene ID: 124416876, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416876
Gene description
Sharpr-MPRA regulatory region 3512
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 was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124416876 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (97072832..97073126)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (97953724..97954018)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (98832589..98832883)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr10.3525 Neighboring gene uncharacterized LOC102723665 Neighboring gene H3K27ac hESC enhancers GRCh37_chr10:98591864-98592578 and GRCh37_chr10:98592579-98593294 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:98593295-98594008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98597029-98597529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98599567-98600066 Neighboring gene Sharpr-MPRA regulatory region 4280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98602601-98603100 Neighboring gene ligand dependent nuclear receptor corepressor Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 35 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:98744001-98744502 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:98744503-98745002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98761702-98762390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98780664-98781497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98790940-98791510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98791511-98792081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:98794025-98794781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98797839-98798339 Neighboring gene slit guidance ligand 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2666 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:98829552-98830751 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:98839846-98840622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98850461-98851078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98860158-98861022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98861023-98861885 Neighboring gene SLIT1 antisense RNA 1 Neighboring gene MPRA-validated peak1061 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98890534-98891034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98900602-98901342 Neighboring gene ARHGAP19-SLIT1 readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:98922776-98923310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:98923311-98923844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98923845-98924378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98945560-98946060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98946061-98946561 Neighboring gene uncharacterized LOC112268065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2668 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:98962904-98963503

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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_079098.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    97072832..97073126
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    97953724..97954018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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