LOC130058203 (ATAC-STARR-seq lymphoblastoid silent region 7014) - Rat Genome Database

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Gene: LOC130058203 (ATAC-STARR-seq lymphoblastoid silent region 7014) Homo sapiens
Analyze
Symbol: LOC130058203
Name: ATAC-STARR-seq lymphoblastoid silent region 7014
RGD ID: 329835279
Description: 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]
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
GRCh38161,983,945 - 1,984,484 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37162,033,946 - 2,034,485 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.0162,003,890 - 2,004,429 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130058203
54 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 16p13.3(chr16:46766-1997582)x1 copy number loss See cases [RCV000053253] Chr16:46766..1997582 [GRCh38]
Chr16:96766..2047583 [GRCh37]
Chr16:36766..1987584 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3-13.13(chr16:23141-11296695)x3 copy number gain See cases [RCV000052367] Chr16:23141..11296695 [GRCh38]
Chr16:73141..11390552 [GRCh37]
Chr16:13141..11298053 [NCBI36]
Chr16:16p13.3-13.13		 pathogenic
GRCh38/hg38 16p13.3(chr16:29941-2560460)x3 copy number gain See cases [RCV000052368] Chr16:29941..2560460 [GRCh38]
Chr16:79941..2610461 [GRCh37]
Chr16:19941..2550462 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3(chr16:46766-3214623)x3 copy number gain See cases [RCV000052370] Chr16:46766..3214623 [GRCh38]
Chr16:96766..3264623 [GRCh37]
Chr16:36766..3204624 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3(chr16:1221651-2233773)x3 copy number gain See cases [RCV000052373] Chr16:1221651..2233773 [GRCh38]
Chr16:1271651..2283774 [GRCh37]
Chr16:1211652..2223775 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3(chr16:1816283-2020966)x3 copy number gain See cases [RCV000052377] Chr16:1816283..2020966 [GRCh38]
Chr16:1866284..2070967 [GRCh37]
Chr16:1806285..2010968 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3(chr16:46766-4247185)x3 copy number gain See cases [RCV000136687] Chr16:46766..4247185 [GRCh38]
Chr16:96766..4297186 [GRCh37]
Chr16:36766..4237187 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3(chr16:1850978-2116369)x3 copy number gain See cases [RCV000135695] Chr16:1850978..2116369 [GRCh38]
Chr16:1900979..2166370 [GRCh37]
Chr16:1840980..2106371 [NCBI36]
Chr16:16p13.3		 uncertain significance
GRCh38/hg38 16p13.3-13.13(chr16:46766-11525516)x3 copy number gain See cases [RCV000133780] Chr16:46766..11525516 [GRCh38]
Chr16:96766..11619372 [GRCh37]
Chr16:36766..11526873 [NCBI36]
Chr16:16p13.3-13.13		 pathogenic
GRCh38/hg38 16p13.3-13.12(chr16:43732-13326806)x3 copy number gain See cases [RCV000139166] Chr16:43732..13326806 [GRCh38]
Chr16:93732..13420663 [GRCh37]
Chr16:33732..13328164 [NCBI36]
Chr16:16p13.3-13.12		 pathogenic
GRCh38/hg38 16p13.3-13.11(chr16:666662-15743104)x3 copy number gain See cases [RCV000143710] Chr16:666662..15743104 [GRCh38]
Chr16:716662..15836961 [GRCh37]
Chr16:656663..15744462 [NCBI36]
Chr16:16p13.3-13.11		 pathogenic
NM_005262.3(GFER):c.189G>C (p.Glu63Asp) single nucleotide variant Congenital cataract-progressive muscular hypotonia-hearing loss-developmental delay syndrome [RCV003619661]|GFER-related disorder [RCV003937733]|Inborn genetic diseases [RCV002517217]|not provided [RCV000676336] Chr16:1984407 [GRCh38]
Chr16:2034408 [GRCh37]
Chr16:16p13.3		 likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_005262.3(GFER):c.245G>A (p.Arg82Gln) single nucleotide variant not provided [RCV000198190] Chr16:1984463 [GRCh38]
Chr16:2034464 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.57G>C (p.Pro19=) single nucleotide variant GFER-related disorder [RCV004758668]|not provided [RCV000907861]|not specified [RCV000196063] Chr16:1984275 [GRCh38]
Chr16:2034276 [GRCh37]
Chr16:16p13.3		 benign
NM_005262.3(GFER):c.199del (p.Arg67fs) deletion Congenital cataract-progressive muscular hypotonia-hearing loss-developmental delay syndrome [RCV001270124]|Mitochondrial disease [RCV000508880]|not provided [RCV000200750] Chr16:1984415 [GRCh38]
Chr16:2034416 [GRCh37]
Chr16:16p13.3		 pathogenic|likely pathogenic|conflicting interpretations of pathogenicity
NM_005262.3(GFER):c.14G>C (p.Gly5Ala) single nucleotide variant not provided [RCV002515403]|not specified [RCV000199610] Chr16:1984232 [GRCh38]
Chr16:2034233 [GRCh37]
Chr16:16p13.3		 likely pathogenic|likely benign|uncertain significance
NM_005262.3(GFER):c.217G>T (p.Ala73Ser) single nucleotide variant not provided [RCV004770963] Chr16:1984435 [GRCh38]
Chr16:2034436 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.25del (p.Arg9fs) deletion not provided [RCV000487913] Chr16:1984242 [GRCh38]
Chr16:2034243 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.2(GFER):c.-55_-44delGACCTGGAGGCT deletion not specified [RCV000610288] Chr16:1984154..1984165 [GRCh38]
Chr16:2034155..2034166 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.12C>T (p.Pro4=) single nucleotide variant not provided [RCV002528685]|not specified [RCV000610908] Chr16:1984230 [GRCh38]
Chr16:2034231 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.217del (p.Ala73fs) deletion Congenital cataract-progressive muscular hypotonia-hearing loss-developmental delay syndrome [RCV000679993]|not provided [RCV000676337] Chr16:1984433 [GRCh38]
Chr16:2034434 [GRCh37]
Chr16:16p13.3		 pathogenic|likely pathogenic
NM_005262.3(GFER):c.219del (p.Cys74fs) deletion Congenital cataract-progressive muscular hypotonia-hearing loss-developmental delay syndrome [RCV000824904] Chr16:1984436 [GRCh38]
Chr16:2034437 [GRCh37]
Chr16:16p13.3		 pathogenic|likely pathogenic
NM_005262.2(GFER):c.-250C>G single nucleotide variant not provided [RCV000830817] Chr16:1983969 [GRCh38]
Chr16:2033970 [GRCh37]
Chr16:16p13.3		 benign
NM_005262.2(GFER):c.-83C>T single nucleotide variant not provided [RCV000830818] Chr16:1984136 [GRCh38]
Chr16:2034137 [GRCh37]
Chr16:16p13.3		 benign
NM_005262.2(GFER):c.-75C>G single nucleotide variant not provided [RCV000832936] Chr16:1984144 [GRCh38]
Chr16:2034145 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.2(GFER):c.-150G>A single nucleotide variant not provided [RCV000832987] Chr16:1984069 [GRCh38]
Chr16:2034070 [GRCh37]
Chr16:16p13.3		 benign
NM_005262.3(GFER):c.129C>T (p.Asp43=) single nucleotide variant not provided [RCV000941915] Chr16:1984347 [GRCh38]
Chr16:2034348 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.90G>A (p.Leu30=) single nucleotide variant not provided [RCV000928129] Chr16:1984308 [GRCh38]
Chr16:2034309 [GRCh37]
Chr16:16p13.3		 likely benign
NC_000016.10:g.1851807_2093151del deletion Tuberous sclerosis 2 [RCV001257345] Chr16:1851807..2093151 [GRCh38]
Chr16:16p13.3		 pathogenic
NC_000016.10:g.1984018_1984019insCCGCCCCGGCC insertion not provided [RCV001537041] Chr16:1984011..1984012 [GRCh38]
Chr16:2034012..2034013 [GRCh37]
Chr16:16p13.3		 benign
NM_005262.3(GFER):c.216G>A (p.Arg72=) single nucleotide variant not provided [RCV001824539] Chr16:1984434 [GRCh38]
Chr16:2034435 [GRCh37]
Chr16:16p13.3		 conflicting interpretations of pathogenicity|uncertain significance
NM_005262.3(GFER):c.34G>A (p.Gly12Ser) single nucleotide variant Inborn genetic diseases [RCV002550414]|not provided [RCV001874341] Chr16:1984252 [GRCh38]
Chr16:2034253 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.236C>A (p.Thr79Lys) single nucleotide variant not provided [RCV001923752] Chr16:1984454 [GRCh38]
Chr16:2034455 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.199C>T (p.Arg67Trp) single nucleotide variant not provided [RCV002038484] Chr16:1984417 [GRCh38]
Chr16:2034418 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.138C>T (p.Ala46=) single nucleotide variant not provided [RCV002145982] Chr16:1984356 [GRCh38]
Chr16:2034357 [GRCh37]
Chr16:16p13.3		 likely benign
NC_000016.10:g.1903155_2093402del deletion Tuberous sclerosis 2 [RCV002267197] Chr16:1903155..2093402 [GRCh38]
Chr16:16p13.3		 pathogenic
NM_005262.3(GFER):c.173A>G (p.Asp58Gly) single nucleotide variant not provided [RCV002291891] Chr16:1984391 [GRCh38]
Chr16:2034392 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.258+1G>A single nucleotide variant Congenital cataract-progressive muscular hypotonia-hearing loss-developmental delay syndrome [RCV002471905]|not provided [RCV002573620] Chr16:1984477 [GRCh38]
Chr16:2034478 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.127G>T (p.Asp43Tyr) single nucleotide variant Inborn genetic diseases [RCV002622026]|not provided [RCV002614339] Chr16:1984345 [GRCh38]
Chr16:2034346 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.56C>T (p.Pro19Leu) single nucleotide variant not provided [RCV002681510] Chr16:1984274 [GRCh38]
Chr16:2034275 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.72C>T (p.Ser24=) single nucleotide variant not provided [RCV002681943] Chr16:1984290 [GRCh38]
Chr16:2034291 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.6G>C (p.Ala2=) single nucleotide variant not provided [RCV002846902] Chr16:1984224 [GRCh38]
Chr16:2034225 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.209C>G (p.Pro70Arg) single nucleotide variant Inborn genetic diseases [RCV002978158] Chr16:1984427 [GRCh38]
Chr16:2034428 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.181G>C (p.Val61Leu) single nucleotide variant not provided [RCV003040113] Chr16:1984399 [GRCh38]
Chr16:2034400 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.45C>G (p.Leu15=) single nucleotide variant not provided [RCV002848398] Chr16:1984263 [GRCh38]
Chr16:2034264 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.168C>T (p.Thr56=) single nucleotide variant not provided [RCV002663675] Chr16:1984386 [GRCh38]
Chr16:2034387 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.37G>C (p.Gly13Arg) single nucleotide variant not provided [RCV002871792] Chr16:1984255 [GRCh38]
Chr16:2034256 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.61G>A (p.Gly21Ser) single nucleotide variant Inborn genetic diseases [RCV002893672] Chr16:1984279 [GRCh38]
Chr16:2034280 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.193G>A (p.Ala65Thr) single nucleotide variant not provided [RCV002852868] Chr16:1984411 [GRCh38]
Chr16:2034412 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.51C>T (p.Phe17=) single nucleotide variant not provided [RCV002642416] Chr16:1984269 [GRCh38]
Chr16:2034270 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.129C>A (p.Asp43Glu) single nucleotide variant not provided [RCV002626887] Chr16:1984347 [GRCh38]
Chr16:2034348 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.254A>G (p.Gln85Arg) single nucleotide variant Inborn genetic diseases [RCV002934090] Chr16:1984472 [GRCh38]
Chr16:2034473 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.116C>T (p.Ala39Val) single nucleotide variant not provided [RCV002918678] Chr16:1984334 [GRCh38]
Chr16:2034335 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.63C>T (p.Gly21=) single nucleotide variant not provided [RCV002627459] Chr16:1984281 [GRCh38]
Chr16:2034282 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.133G>A (p.Ala45Thr) single nucleotide variant Inborn genetic diseases [RCV004064394]|not provided [RCV002576299] Chr16:1984351 [GRCh38]
Chr16:2034352 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.137C>T (p.Ala46Val) single nucleotide variant not provided [RCV002745665] Chr16:1984355 [GRCh38]
Chr16:2034356 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.146C>G (p.Ser49Trp) single nucleotide variant Inborn genetic diseases [RCV002713759] Chr16:1984364 [GRCh38]
Chr16:2034365 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.35G>C (p.Gly12Ala) single nucleotide variant not provided [RCV002627057] Chr16:1984253 [GRCh38]
Chr16:2034254 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.112G>A (p.Gly38Ser) single nucleotide variant not provided [RCV002937807] Chr16:1984330 [GRCh38]
Chr16:2034331 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.55C>T (p.Pro19Ser) single nucleotide variant not provided [RCV003071856]|not specified [RCV003317645] Chr16:1984273 [GRCh38]
Chr16:2034274 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.53T>G (p.Leu18Arg) single nucleotide variant not provided [RCV002608151] Chr16:1984271 [GRCh38]
Chr16:2034272 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.42C>G (p.Asn14Lys) single nucleotide variant Inborn genetic diseases [RCV004064555]|not provided [RCV002581317] Chr16:1984260 [GRCh38]
Chr16:2034261 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.18G>C (p.Glu6Asp) single nucleotide variant not provided [RCV002631902] Chr16:1984236 [GRCh38]
Chr16:2034237 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.205C>A (p.Arg69=) single nucleotide variant not provided [RCV003112354] Chr16:1984423 [GRCh38]
Chr16:2034424 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.36C>T (p.Gly12=) single nucleotide variant not provided [RCV003121193] Chr16:1984254 [GRCh38]
Chr16:2034255 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.68G>C (p.Arg23Pro) single nucleotide variant not provided [RCV003126986] Chr16:1984286 [GRCh38]
Chr16:2034287 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.136G>C (p.Ala46Pro) single nucleotide variant Inborn genetic diseases [RCV003290491] Chr16:1984354 [GRCh38]
Chr16:2034355 [GRCh37]
Chr16:16p13.3		 uncertain significance
NM_005262.3(GFER):c.153A>T (p.Pro51=) single nucleotide variant not provided [RCV003662778] Chr16:1984371 [GRCh38]
Chr16:2034372 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.186C>G (p.Ala62=) single nucleotide variant not provided [RCV003717017] Chr16:1984404 [GRCh38]
Chr16:2034405 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.42C>T (p.Asn14=) single nucleotide variant not provided [RCV003817039] Chr16:1984260 [GRCh38]
Chr16:2034261 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.9G>A (p.Ala3=) single nucleotide variant not provided [RCV003725547] Chr16:1984227 [GRCh38]
Chr16:2034228 [GRCh37]
Chr16:16p13.3		 likely benign
NM_005262.3(GFER):c.41A>C (p.Asn14Thr) single nucleotide variant Inborn genetic diseases [RCV004387782] Chr16:1984259 [GRCh38]
Chr16:2034260 [GRCh37]
Chr16:16p13.3		 uncertain significance

Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130058203 COSMIC
GTEx LOC130058203 GTEx
Human Proteome Map LOC130058203 Human Proteome Map
NCBI Gene LOC130058203 ENTREZGENE