LOC129997861 (ATAC-STARR-seq lymphoblastoid active region 25565) - Rat Genome Database

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Gene: LOC129997861 (ATAC-STARR-seq lymphoblastoid active region 25565) Homo sapiens
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Symbol: LOC129997861
Name: ATAC-STARR-seq lymphoblastoid active region 25565
RGD ID: 329823024
Description: This genomic sequence represents an accessible chromatin region 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3874,775,702 - 4,775,771 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3774,815,333 - 4,815,402 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.074,892,916 - 4,892,985 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC129997861
9 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 7p22.2-22.1(chr7:4469558-5111872)x3 copy number gain See cases [RCV000050969] Chr7:4469558..5111872 [GRCh38]
Chr7:4509189..5151503 [GRCh37]
Chr7:4475715..5118029 [NCBI36]
Chr7:7p22.2-22.1		 uncertain significance
NM_014855.3(AP5Z1):c.8C>T (p.Ser3Leu) single nucleotide variant Hereditary spastic paraplegia 48 [RCV001964866]|not provided [RCV003481196] Chr7:4775723 [GRCh38]
Chr7:4815354 [GRCh37]
Chr7:7p22.1		 uncertain significance
NM_014855.3(AP5Z1):c.37G>C (p.Ala13Pro) single nucleotide variant not provided [RCV001663574] Chr7:4775752 [GRCh38]
Chr7:4815383 [GRCh37]
Chr7:7p22.1		 uncertain significance
NM_014855.3(AP5Z1):c.-3G>A single nucleotide variant AP5Z1-related disorder [RCV003922600]|Hereditary spastic paraplegia 48 [RCV000291097]|Hereditary spastic paraplegia [RCV001848702]|not provided [RCV001591026] Chr7:4775713 [GRCh38]
Chr7:4815344 [GRCh37]
Chr7:7p22.1		 benign|likely benign|uncertain significance
NM_014855.3(AP5Z1):c.-1G>C single nucleotide variant Hereditary spastic paraplegia 48 [RCV001164610]|Hereditary spastic paraplegia [RCV001849070]|not provided [RCV000710600] Chr7:4775715 [GRCh38]
Chr7:4815346 [GRCh37]
Chr7:7p22.1		 likely benign
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:54185-26827634)x3 copy number gain See cases [RCV000136557] Chr7:54185..26827634 [GRCh38]
Chr7:54185..26867253 [GRCh37]
Chr7:149268..26833778 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
NM_014855.3(AP5Z1):c.41+5G>T single nucleotide variant Hereditary spastic paraplegia 48 [RCV002667048] Chr7:4775761 [GRCh38]
Chr7:4815392 [GRCh37]
Chr7:7p22.1		 uncertain significance
NM_014855.3(AP5Z1):c.41+15C>T single nucleotide variant Hereditary spastic paraplegia 48 [RCV002975024] Chr7:4775771 [GRCh38]
Chr7:4815402 [GRCh37]
Chr7:7p22.1		 likely benign
GRCh38/hg38 7p22.3-22.1(chr7:54185-6638027)x3 copy number gain See cases [RCV000136731] Chr7:54185..6638027 [GRCh38]
Chr7:54185..6677658 [GRCh37]
Chr7:149268..6644183 [NCBI36]
Chr7:7p22.3-22.1		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:1698124-27207295)x3 copy number gain See cases [RCV000143060] Chr7:1698124..27207295 [GRCh38]
Chr7:1737760..27246914 [GRCh37]
Chr7:1704286..27213439 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
NM_014855.3(AP5Z1):c.41+8_41+9del deletion Hereditary spastic paraplegia 48 [RCV003060304] Chr7:4775761..4775762 [GRCh38]
Chr7:4815392..4815393 [GRCh37]
Chr7:7p22.1		 likely benign
GRCh38/hg38 7p22.3-21.3(chr7:45130-7252065)x3 copy number gain See cases [RCV000137524] Chr7:45130..7252065 [GRCh38]
Chr7:45130..7291696 [GRCh37]
Chr7:140213..7258221 [NCBI36]
Chr7:7p22.3-21.3		 pathogenic
NM_014855.3(AP5Z1):c.41+9G>A single nucleotide variant Hereditary spastic paraplegia 48 [RCV003073564] Chr7:4775765 [GRCh38]
Chr7:4815396 [GRCh37]
Chr7:7p22.1		 likely benign
GRCh38/hg38 7p22.3-15.3(chr7:45130-25221165)x3 copy number gain See cases [RCV000137824] Chr7:45130..25221165 [GRCh38]
Chr7:45130..25260784 [GRCh37]
Chr7:140213..25227309 [NCBI36]
Chr7:7p22.3-15.3		 pathogenic
GRCh38/hg38 7p22.3-22.1(chr7:45130-5880375)x1 copy number loss See cases [RCV000052249] Chr7:45130..5880375 [GRCh38]
Chr7:45130..5920006 [GRCh37]
Chr7:140213..5886532 [NCBI36]
Chr7:7p22.3-22.1		 pathogenic
GRCh38/hg38 7p22.3-22.1(chr7:45130-6270185)x3 copy number gain See cases [RCV000053527] Chr7:45130..6270185 [GRCh38]
Chr7:45130..6309816 [GRCh37]
Chr7:140213..6276341 [NCBI36]
Chr7:7p22.3-22.1		 pathogenic
GRCh38/hg38 7p22.3-14.2(chr7:54185-37089712)x3 copy number gain See cases [RCV000053530] Chr7:54185..37089712 [GRCh38]
Chr7:54185..37129317 [GRCh37]
Chr7:149268..37095842 [NCBI36]
Chr7:7p22.3-14.2		 pathogenic
NM_014855.3(AP5Z1):c.33C>T (p.His11=) single nucleotide variant AP5Z1-related disorder [RCV003951667] Chr7:4775748 [GRCh38]
Chr7:4815379 [GRCh37]
Chr7:7p22.1		 likely benign
NM_014855.3(AP5Z1):c.22A>C (p.Ser8Arg) single nucleotide variant Hereditary spastic paraplegia 48 [RCV001045206] Chr7:4775737 [GRCh38]
Chr7:4815368 [GRCh37]
Chr7:7p22.1		 uncertain significance
GRCh38/hg38 7p22.3-14.1(chr7:54185-41875885)x3 copy number gain See cases [RCV000051159] Chr7:54185..41875885 [GRCh38]
Chr7:54185..41915483 [GRCh37]
Chr7:149268..41882008 [NCBI36]
Chr7:7p22.3-14.1		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:43360-27196404)x3 copy number gain See cases [RCV000143586] Chr7:43360..27196404 [GRCh38]
Chr7:43360..27236023 [GRCh37]
Chr7:138443..27202548 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1643402BMD2_HBone mineral density QTL 2 (human)2.690.0002Bone mineral density7122435431Human
1643247BW130_HBody Weight QTL 130 (human)1.280.008Body weightbody mass index7117453493Human
1643391BW322_HBody weight QTL 322 (human)2.690.0002Body fat amount7122435431Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129997861 COSMIC
GTEx LOC129997861 GTEx
Human Proteome Map LOC129997861 Human Proteome Map
NCBI Gene LOC129997861 ENTREZGENE