Variant report

Variant	rs4858992
Chromosome Location	chr3:88123780-88123781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88106550..88112808-chr3:88121640..88129198,13	MCF-7	breast:
2	chr3:88123411..88125360-chr3:88127361..88130241,2	K562	blood:
3	chr3:88111449..88113994-chr3:88120532..88124879,4	K562	blood:

Variant related genes	Relation type
ENSG00000229729	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 163 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs1006895	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040319	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1051413	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051436	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063597	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063603	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865625	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495016	0.97[EUR][1000 genomes]
rs12632529	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058811	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13060730	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063511	0.89[ASN][1000 genomes]
rs13067419	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13076170	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098157	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991659	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049817	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116149	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732776	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3890707	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4241551	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4257571	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4273396	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4276211	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4276212	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4337654	0.86[ASN][1000 genomes]
rs4368523	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374552	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4378991	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384978	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4402954	0.84[AFR][1000 genomes]
rs4407422	0.81[AFR][1000 genomes]
rs4414876	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4416403	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429658	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4432672	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4434168	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4438681	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485742	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4488864	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4501136	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4502603	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507280	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4518156	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4555548	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4568164	0.81[ASN][1000 genomes]
rs4580585	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4588391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596173	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4611846	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616670	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4638995	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858931	0.91[ASN][1000 genomes]
rs4858936	0.82[ASN][1000 genomes]
rs4858981	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858982	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858983	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858985	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858994	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858995	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4858997	0.80[AFR][1000 genomes]
rs4858998	0.89[ASN][1000 genomes]
rs4858999	0.89[ASN][1000 genomes]
rs4859001	0.82[ASN][1000 genomes]
rs5024148	0.80[AFR][1000 genomes]
rs5024149	0.80[AFR][1000 genomes]
rs6419867	0.83[ASN][1000 genomes]
rs6551266	0.80[EUR][1000 genomes]
rs6551268	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6551271	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6551272	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6551273	0.89[ASN][1000 genomes]
rs6551274	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6551275	0.86[ASN][1000 genomes]
rs6551277	0.86[ASN][1000 genomes]
rs6551278	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6551282	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6551283	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6551284	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6551285	0.81[ASN][1000 genomes]
rs6551286	0.82[ASN][1000 genomes]
rs6551288	0.82[ASN][1000 genomes]
rs6551289	0.82[ASN][1000 genomes]
rs6551291	0.81[ASN][1000 genomes]
rs6767258	0.86[ASN][1000 genomes]
rs6777019	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781333	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6782507	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6785359	0.86[ASN][1000 genomes]
rs6786788	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6787824	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6790426	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790629	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791133	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6792208	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6793783	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6796355	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6799233	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804818	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7427704	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7429120	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7430158	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7433285	0.86[ASN][1000 genomes]
rs7617691	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7618080	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7618472	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626777	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7628689	0.86[ASN][1000 genomes]
rs7630028	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7630240	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7632123	0.81[ASN][1000 genomes]
rs7633121	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7635996	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7639420	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7641173	0.81[ASN][1000 genomes]
rs7643923	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7648096	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650707	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7651641	0.86[ASN][1000 genomes]
rs7651999	0.91[ASN][1000 genomes]
rs7652528	0.82[ASN][1000 genomes]
rs7653652	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9310066	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310072	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9310074	0.91[ASN][1000 genomes]
rs9310077	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs959048	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959049	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959050	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813894	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9814057	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9821517	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832011	0.90[ASN][1000 genomes]
rs9834468	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9834501	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835178	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835771	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836364	0.80[AFR][1000 genomes]
rs9840953	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9841189	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9845776	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846115	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847019	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850892	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851328	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9854138	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9861398	0.89[ASN][1000 genomes]
rs9864220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865335	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9865578	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9865703	0.86[ASN][1000 genomes]
rs9865710	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9865990	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866349	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870952	0.90[AFR][1000 genomes]
rs9872602	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879044	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881255	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4858992	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs4858992	C3orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88109400-88124400	Weak transcription	Pancreas	Pancrea
2	chr3:88110200-88124200	Weak transcription	Fetal Kidney	kidney
3	chr3:88111400-88124200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:88111400-88133600	Weak transcription	Brain Angular Gyrus	brain
5	chr3:88111400-88136200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:88111400-88136200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:88111600-88124000	Weak transcription	Right Atrium	heart
8	chr3:88111600-88124000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:88111600-88124000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:88111600-88124200	Weak transcription	Fetal Lung	lung
11	chr3:88111600-88135200	Weak transcription	HSMM	muscle
12	chr3:88111600-88135400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:88111600-88135600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:88111800-88135400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:88112200-88136600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:88112200-88154200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:88112400-88124400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:88112400-88143600	Weak transcription	HUVEC	blood vessel
19	chr3:88113200-88146200	Weak transcription	HMEC	breast
20	chr3:88113800-88134800	Weak transcription	Dnd41	blood
21	chr3:88115200-88133400	Weak transcription	Left Ventricle	heart
22	chr3:88115600-88124000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:88116800-88124200	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:88116800-88139800	Weak transcription	Thymus	Thymus
25	chr3:88117000-88124400	Weak transcription	Right Ventricle	heart
26	chr3:88117000-88133800	Weak transcription	Aorta	Aorta
27	chr3:88117000-88135800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:88117400-88124600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:88117600-88123800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:88118000-88124200	Weak transcription	Fetal Heart	heart
31	chr3:88118000-88128800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:88118200-88124000	Weak transcription	K562	blood
33	chr3:88118800-88124200	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:88120600-88128600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:88120600-88135400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:88121000-88135400	Weak transcription	Fetal Thymus	thymus
37	chr3:88121400-88136400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:88121600-88129000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:88121600-88130200	Weak transcription	Primary B cells from cord blood	blood
40	chr3:88121800-88123800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:88121800-88130800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:88121800-88141800	Weak transcription	NHLF	lung
43	chr3:88122200-88124800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:88122400-88123800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:88122400-88124000	Weak transcription	Brain Substantia Nigra	brain
46	chr3:88122400-88130200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:88122600-88124000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:88122600-88125000	Weak transcription	GM12878-XiMat	blood
49	chr3:88122800-88124600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr3:88122800-88127400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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