Variant report

Variant	rs17364076
Chromosome Location	chr15:76760891-76760892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs11072599	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072603	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1117367	0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1125932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12148786	0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12148805	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12437627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12438077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs12439484	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs12440815	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12441247	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12441433	0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12441550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12442266	0.82[JPT][hapmap]
rs12443137	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12591100	0.84[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs12592171	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592386	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12592420	0.92[ASN][1000 genomes]
rs12593751	0.98[ASN][1000 genomes]
rs12594212	0.85[ASN][1000 genomes]
rs12594577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12898415	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs12899871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12902174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12902414	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907668	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12907805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908334	0.88[JPT][hapmap]
rs12911987	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12914005	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915248	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916573	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12917430	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157783	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs1587381	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603856	1.00[YRI][hapmap]
rs17361504	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs17362383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17363364	1.00[YRI][hapmap]
rs17363713	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17364330	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364714	1.00[YRI][hapmap]
rs17458234	1.00[YRI][hapmap]
rs17460201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17461634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867197	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1874944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1875884	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1875885	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1946650	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1965492	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2083762	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs2117369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120107	0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2120108	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2164101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176623	1.00[ASW][hapmap];0.83[JPT][hapmap]
rs2404740	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs284892	0.81[AMR][1000 genomes]
rs284895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759853	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs3866543	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4079681	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4633676	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4886496	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886799	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4886801	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4886813	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4886817	0.90[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4886818	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs56089215	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56216512	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56351018	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57178708	0.84[AFR][1000 genomes]
rs58511211	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58684938	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66754747	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs66986092	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67204011	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs67232575	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67263359	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67418609	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs67888330	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67920045	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7162455	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7163946	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165025	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7179142	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7403276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs744336	0.95[MEX][hapmap];0.84[TSI][hapmap]
rs8025134	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8036703	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap]
rs8039545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8043057	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9646213	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17364076	SCAPER	cis	cerebellum	SCAN
rs17364076	NRG4	cis	parietal	SCAN
rs17364076	SCAPER	cis	Artery Tibial	GTEx
rs17364076	STOML1	cis	cerebellum	SCAN
rs17364076	ZNF291	cis	multi-tissue	Pritchard
rs17364076	SCAPER	cis	parietal	SCAN
rs17364076	SCAPER	cis	lung	GTEx
rs17364076	SCAPER	cis	Thyroid	GTEx
rs17364076	SCAPER	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76711600-76767200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:76720800-76763600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
4	chr15:76742800-76762400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:76750400-76763800	Weak transcription	Placenta	Placenta
6	chr15:76753200-76762800	Weak transcription	Esophagus	oesophagus
7	chr15:76753600-76761600	Weak transcription	Adipose Nuclei	Adipose
8	chr15:76753800-76764400	Weak transcription	Fetal Intestine Large	intestine
9	chr15:76754000-76764400	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:76754200-76763600	Weak transcription	Pancreas	Pancrea
11	chr15:76754400-76763600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:76754800-76762000	Weak transcription	Ovary	ovary
13	chr15:76754800-76764400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:76755200-76761200	Weak transcription	Brain Anterior Caudate	brain
15	chr15:76755600-76764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:76757800-76765200	Weak transcription	Aorta	Aorta
17	chr15:76758400-76765600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr15:76758600-76761200	Weak transcription	Fetal Heart	heart
19	chr15:76758600-76762400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:76758800-76764400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:76758800-76765000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:76758800-76765200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:76759000-76761000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr15:76759200-76762600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:76759200-76763800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:76759200-76764400	Weak transcription	Psoas Muscle	Psoas
27	chr15:76759400-76761800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:76759400-76762600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:76759400-76763600	Strong transcription	Liver	Liver
30	chr15:76759400-76764400	Weak transcription	Fetal Muscle Leg	muscle
31	chr15:76759600-76761000	Weak transcription	Primary T cells from cord blood	blood
32	chr15:76759600-76761200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr15:76759800-76761800	Weak transcription	Dnd41	blood
34	chr15:76759800-76762800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:76759800-76763400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:76759800-76770400	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:76760000-76762400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:76760000-76772600	Weak transcription	GM12878-XiMat	blood
39	chr15:76760200-76761000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:76760200-76761200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr15:76760400-76773800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:76760600-76761200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:76760600-76763000	Weak transcription	Right Ventricle	heart
44	chr15:76760600-76764200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr15:76760800-76761000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
46	chr15:76760800-76763000	Strong transcription	Primary B cells from cord blood	blood
47	chr15:76760800-76763000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr15:76760800-76763400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:76760800-76763400	Weak transcription	Brain Angular Gyrus	brain
50	chr15:76760800-76764200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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