LOC109648316 RUNX1 element RE2 [Homo sapiens (human)] - Gene

Summary

Gene symbol: LOC109648316
Gene description: RUNX1 element RE2
Gene type: biological region
Feature type(s): protein_bind
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: This genomic region represents a conserved sequence located in the fifth intron of the runt related transcription factor 1 (RUNX1) gene. It was shown to have physical interactions with the RUNX1 P1 and P2 promoters and may be important for RUNX1 transcription. A subregion was validated as an enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it was defined as a group 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. An overlapping subregion was also shown to function as an enhancer in K562 erythroleukemia cells. Naturally occurring polymorphisms in that subregion are associated with acute myeloid leukemia and may influence the ability of this sequence to function as an enhancer. Another subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

Location:: chromosome: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (34807270..34808855)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (33189876..33191461)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (36180628..36181138)

Chromosome 21 - NC_000021.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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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

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General gene information

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Other Names

ATAC-STARR-seq lymphoblastoid active region 18401
H3K4me1 hESC enhancer GRCh37_chr21:36180653-36181152
MED14-independent group 3 enhancer GRCh37_chr21:36179567-36180766
RUNX1 intron 5.2 enhancer

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.