LOC130056973 (ATAC-STARR-seq lymphoblastoid active region 9341) - Rat Genome Database

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Gene: LOC130056973 (ATAC-STARR-seq lymphoblastoid active region 9341) Homo sapiens
Analyze
Symbol: LOC130056973
Name: ATAC-STARR-seq lymphoblastoid active region 9341
RGD ID: 329834058
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
GRCh381544,596,199 - 44,596,348 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01542,404,168 - 42,404,317 (+)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 LOC130056973
46 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_025137.4(SPG11):c.4187G>T (p.Ser1396Ile) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001959694] Chr15:44596330 [GRCh38]
Chr15:44888528 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4232C>T (p.Pro1411Leu) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001916407] Chr15:44596285 [GRCh38]
Chr15:44888483 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4253T>A (p.Met1418Lys) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001249244]|not provided [RCV001751509] Chr15:44596264 [GRCh38]
Chr15:44888462 [GRCh37]
Chr15:15q21.1		 uncertain significance|not provided
NM_025137.4(SPG11):c.4201G>C (p.Asp1401His) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001923264] Chr15:44596316 [GRCh38]
Chr15:44888514 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4284C>A (p.Pro1428=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV002539947] Chr15:44596233 [GRCh38]
Chr15:44888431 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4291del (p.Leu1431fs) deletion Inborn genetic diseases [RCV002330220] Chr15:44596226 [GRCh38]
Chr15:44888424 [GRCh37]
Chr15:15q21.1		 pathogenic
NM_025137.4(SPG11):c.4300A>G (p.Ser1434Gly) single nucleotide variant Inborn genetic diseases [RCV002331892] Chr15:44596217 [GRCh38]
Chr15:44888415 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4185C>G (p.Phe1395Leu) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001977466] Chr15:44596332 [GRCh38]
Chr15:44888530 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4304A>G (p.Lys1435Arg) single nucleotide variant Hereditary spastic paraplegia 11 [RCV002050647]|Inborn genetic diseases [RCV002543496] Chr15:44596213 [GRCh38]
Chr15:44888411 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4227C>G (p.Asn1409Lys) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001996838] Chr15:44596290 [GRCh38]
Chr15:44888488 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4287G>A (p.Gln1429=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV002064602] Chr15:44596230 [GRCh38]
Chr15:44888428 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4206C>T (p.His1402=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV002746365] Chr15:44596311 [GRCh38]
Chr15:44888509 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4185C>T (p.Phe1395=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV002711137] Chr15:44596332 [GRCh38]
Chr15:44888530 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4200A>G (p.Gln1400=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV002900609] Chr15:44596317 [GRCh38]
Chr15:44888515 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4198C>A (p.Gln1400Lys) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003023306] Chr15:44596319 [GRCh38]
Chr15:44888517 [GRCh37]
Chr15:15q21.1		 uncertain significance
NC_000015.10:g.44330225_44821972dup duplication See cases [RCV003313908] Chr15:44330225..44821972 [GRCh38]
Chr15:15q15.3-21.1		 uncertain significance
NM_025137.4(SPG11):c.4204C>A (p.His1402Asn) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001884216] Chr15:44596313 [GRCh38]
Chr15:44888511 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4215G>A (p.Leu1405=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV002135438] Chr15:44596302 [GRCh38]
Chr15:44888500 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4230G>A (p.Leu1410=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003002841] Chr15:44596287 [GRCh38]
Chr15:44888485 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4317C>T (p.Thr1439=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001447058] Chr15:44596200 [GRCh38]
Chr15:44888398 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4307_4308del (p.Gln1436fs) deletion Hereditary spastic paraplegia 11 [RCV000034216]|Inborn genetic diseases [RCV002326720]|not provided [RCV000517443] Chr15:44596209..44596210 [GRCh38]
Chr15:44888407..44888408 [GRCh37]
Chr15:15q21.1		 pathogenic
NM_025137.4(SPG11):c.4231C>T (p.Pro1411Ser) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001040767] Chr15:44596286 [GRCh38]
Chr15:44888484 [GRCh37]
Chr15:15q21.1		 likely benign|uncertain significance
NM_025137.4(SPG11):c.4284C>G (p.Pro1428=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001492220] Chr15:44596233 [GRCh38]
Chr15:44888431 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4176C>G (p.Ile1392Met) single nucleotide variant not provided [RCV000731320] Chr15:44596341 [GRCh38]
Chr15:44888539 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4260C>T (p.Ser1420=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV000861583] Chr15:44596257 [GRCh38]
Chr15:44888455 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4281C>G (p.Cys1427Trp) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003340987] Chr15:44596236 [GRCh38]
Chr15:44888434 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4308A>G (p.Gln1436=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001482720] Chr15:44596209 [GRCh38]
Chr15:44888407 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4261G>A (p.Asp1421Asn) single nucleotide variant Amyotrophic lateral sclerosis type 5 [RCV002467868]|Charcot-Marie-Tooth disease axonal type 2X [RCV002467869]|Hereditary spastic paraplegia 11 [RCV000556968]|Inborn genetic diseases [RCV002330887]|not provided [RCV002263778] Chr15:44596256 [GRCh38]
Chr15:44888454 [GRCh37]
Chr15:15q21.1		 likely benign|uncertain significance
NM_025137.4(SPG11):c.4309G>C (p.Glu1437Gln) single nucleotide variant Hereditary spastic paraplegia 11 [RCV002549908]|not provided [RCV000995319] Chr15:44596208 [GRCh38]
Chr15:44888406 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4216G>T (p.Ala1406Ser) single nucleotide variant Amyotrophic lateral sclerosis type 5 [RCV002468016]|Charcot-Marie-Tooth disease axonal type 2X [RCV002468017]|Hereditary spastic paraplegia 11 [RCV000702089]|Inborn genetic diseases [RCV002332484]|not provided [RCV000995320] Chr15:44596301 [GRCh38]
Chr15:44888499 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4198C>T (p.Gln1400Ter) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003043855] Chr15:44596319 [GRCh38]
Chr15:44888517 [GRCh37]
Chr15:15q21.1		 pathogenic
NM_025137.4(SPG11):c.4190C>T (p.Pro1397Leu) single nucleotide variant Hereditary spastic paraplegia 11 [RCV000794361] Chr15:44596327 [GRCh38]
Chr15:44888525 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4233C>G (p.Pro1411=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV000808450] Chr15:44596284 [GRCh38]
Chr15:44888482 [GRCh37]
Chr15:15q21.1		 likely benign|uncertain significance
NM_025137.4(SPG11):c.4274A>G (p.Asn1425Ser) single nucleotide variant Hereditary spastic paraplegia 11 [RCV000536401] Chr15:44596243 [GRCh38]
Chr15:44888441 [GRCh37]
Chr15:15q21.1		 uncertain significance
NC_000015.9:g.(?_44881450)_(44925835_?)dup duplication Hereditary spastic paraplegia 11 [RCV000466751] Chr15:44589252..44633637 [GRCh38]
Chr15:44881450..44925835 [GRCh37]
Chr15:15q21.1		 pathogenic
NM_025137.4(SPG11):c.4217del (p.Ala1406fs) deletion not provided [RCV001268724] Chr15:44596300 [GRCh38]
Chr15:44888498 [GRCh37]
Chr15:15q21.1		 pathogenic
NM_025137.4(SPG11):c.4212G>A (p.Arg1404=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001463150] Chr15:44596305 [GRCh38]
Chr15:44888503 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4237delinsTA (p.Val1413fs) indel Hereditary spastic paraplegia 11 [RCV001242891] Chr15:44596280 [GRCh38]
Chr15:44888478 [GRCh37]
Chr15:15q21.1		 pathogenic
NM_025137.4(SPG11):c.4204C>T (p.His1402Tyr) single nucleotide variant Hereditary spastic paraplegia 11 [RCV000277299] Chr15:44596313 [GRCh38]
Chr15:44888511 [GRCh37]
Chr15:15q21.1		 uncertain significance
NM_025137.4(SPG11):c.4245C>T (p.Thr1415=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001445407] Chr15:44596272 [GRCh38]
Chr15:44888470 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4233C>T (p.Pro1411=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV001458131] Chr15:44596284 [GRCh38]
Chr15:44888482 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4281C>T (p.Cys1427=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV002576846] Chr15:44596236 [GRCh38]
Chr15:44888434 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4207T>C (p.Leu1403=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003830683] Chr15:44596310 [GRCh38]
Chr15:44888508 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4245C>G (p.Thr1415=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003601764] Chr15:44596272 [GRCh38]
Chr15:44888470 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4239G>A (p.Val1413=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003601116] Chr15:44596278 [GRCh38]
Chr15:44888476 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4188C>T (p.Ser1396=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003496451] Chr15:44596329 [GRCh38]
Chr15:44888527 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4269C>G (p.Val1423=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003495421] Chr15:44596248 [GRCh38]
Chr15:44888446 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4252del (p.Met1418fs) deletion Hereditary spastic paraplegia 11 [RCV003601296] Chr15:44596265 [GRCh38]
Chr15:44888463 [GRCh37]
Chr15:15q21.1		 pathogenic
NM_025137.4(SPG11):c.4173T>C (p.Leu1391=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003600772] Chr15:44596344 [GRCh38]
Chr15:44888542 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4311G>A (p.Glu1437=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003601661] Chr15:44596206 [GRCh38]
Chr15:44888404 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4272C>T (p.Cys1424=) single nucleotide variant Hereditary spastic paraplegia 11 [RCV003600599] Chr15:44596245 [GRCh38]
Chr15:44888443 [GRCh37]
Chr15:15q21.1		 likely benign
NM_025137.4(SPG11):c.4290dup (p.Leu1431fs) duplication Hereditary spastic paraplegia 11 [RCV001391559] Chr15:44596226..44596227 [GRCh38]
Chr15:44888424..44888425 [GRCh37]
Chr15:15q21.1		 pathogenic
NM_025137.4(SPG11):c.4318G>A (p.Asp1440Asn) single nucleotide variant Hereditary spastic paraplegia 11 [RCV000795634] Chr15:44596199 [GRCh38]
Chr15:44888397 [GRCh37]
Chr15:15q21.1		 uncertain significance
NC_000015.10:g.(?_44595239)_(44600652_?)del deletion Hereditary spastic paraplegia 11 [RCV000642613] Chr15:44595239..44600652 [GRCh38]
Chr15:44887437..44892850 [GRCh37]
Chr15:15q21.1		 pathogenic|likely pathogenic

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130056973 COSMIC
GTEx LOC130056973 GTEx
Human Proteome Map LOC130056973 Human Proteome Map
NCBI Gene LOC130056973 ENTREZGENE