Variant report

Variant	rs17620990
Chromosome Location	chr14:105687771-105687772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr14:105686937-105687823	SK-N-SH	brain:	n/a	n/a
2	EP300	chr14:105686569-105687846	SK-N-SH	brain:	n/a	chr14:105687171-105687187

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:105687326..105689962-chr14:105713390..105716265,3	MCF-7	breast:

Variant related genes	Relation type
BRF1	TF binding region
ENSG00000184887	Chromatin interaction
ENSG00000185024	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10149868	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400759	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11160841	0.83[EUR][1000 genomes]
rs11160842	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11621385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622579	0.98[EUR][1000 genomes]
rs11846022	0.95[EUR][1000 genomes]
rs11850453	0.97[EUR][1000 genomes]
rs12147672	0.81[EUR][1000 genomes]
rs12883636	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12893998	0.92[EUR][1000 genomes]
rs12894144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006918	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006925	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010787	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091919	0.95[EUR][1000 genomes]
rs2091920	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2312741	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477712	0.92[ASN][1000 genomes]
rs28702916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087836	0.95[EUR][1000 genomes]
rs33997228	0.97[EUR][1000 genomes]
rs34448993	0.94[AFR][1000 genomes]
rs34766944	0.95[EUR][1000 genomes]
rs35971653	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784222	0.92[ASN][1000 genomes]
rs3784227	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784228	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784229	0.92[ASN][1000 genomes]
rs3861680	0.80[EUR][1000 genomes]
rs4633652	0.94[EUR][1000 genomes]
rs6576077	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7142008	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7142130	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146872	0.89[EUR][1000 genomes]
rs7147888	0.98[EUR][1000 genomes]
rs7148884	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7151473	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7151532	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7157285	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7159235	0.89[EUR][1000 genomes]
rs7160272	0.98[EUR][1000 genomes]
rs8005029	0.99[EUR][1000 genomes]
rs8005486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010342	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010782	0.89[EUR][1000 genomes]
rs8014544	0.93[EUR][1000 genomes]
rs8020454	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8270	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828345	chr14:105100787-105803170	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	nsv542225	chr14:105133688-105803170	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv542227	chr14:105157572-105803170	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
4	nsv917106	chr14:105339195-105803170	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv902422	chr14:105420215-105803170	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv1052190	chr14:105423761-105722653	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv902423	chr14:105430890-105803170	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
8	nsv456458	chr14:105435649-105690092	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
9	nsv566150	chr14:105435649-105690092	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
10	nsv902424	chr14:105436222-105803170	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
11	nsv902425	chr14:105463936-105690092	Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
12	nsv9175	chr14:105496509-105688941	Enhancers Strong transcription Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	esv2758369	chr14:105513346-105803170	Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
14	esv2760014	chr14:105513346-105803170	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
15	nsv902432	chr14:105587644-105690092	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	esv1797182	chr14:105590971-105696174	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	esv1836064	chr14:105590971-105696174	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv902433	chr14:105596054-105719306	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
19	nsv902439	chr14:105602619-105690092	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
20	nsv902440	chr14:105602619-105699630	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
21	nsv902441	chr14:105602619-105803170	Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv902442	chr14:105602619-105803170	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
23	esv1817919	chr14:105605199-105803170	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
24	nsv530813	chr14:105607701-106453697	Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
25	nsv902451	chr14:105624693-105690092	Bivalent/Poised TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
26	nsv902454	chr14:105633499-105690092	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
27	nsv902455	chr14:105633499-105699630	Genic enhancers Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
28	nsv902456	chr14:105636112-105690092	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
29	nsv902460	chr14:105646179-105731255	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
30	nsv902464	chr14:105654606-105717265	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
31	nsv510651	chr14:105656882-105725155	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
32	nsv566186	chr14:105675701-105779305	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
33	esv3397950	chr14:105686557-105689055	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17620990	BTBD6	cis	Thyroid	GTEx
rs17620990	NUDT14	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105668600-105714200	Weak transcription	HUVEC	blood vessel
2	chr14:105669800-105691200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr14:105669800-105713800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr14:105671400-105697000	Weak transcription	Small Intestine	intestine
5	chr14:105671600-105689400	Weak transcription	NHEK	skin
6	chr14:105672200-105694200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr14:105672400-105713200	Weak transcription	Osteobl	bone
8	chr14:105672600-105695600	Weak transcription	HMEC	breast
9	chr14:105673400-105690000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr14:105673600-105713600	Weak transcription	Stomach Mucosa	stomach
11	chr14:105673800-105689800	Weak transcription	Hela-S3	cervix
12	chr14:105674000-105696000	Strong transcription	Fetal Stomach	stomach
13	chr14:105674000-105698600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr14:105674200-105695800	Strong transcription	Fetal Intestine Small	intestine
15	chr14:105674800-105689600	Weak transcription	K562	blood
16	chr14:105674800-105694200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:105674800-105695400	Strong transcription	Fetal Brain Female	brain
18	chr14:105674800-105696000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr14:105675200-105695800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr14:105675400-105688400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr14:105675400-105693400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr14:105675400-105693800	Strong transcription	Primary T cells from cord blood	blood
23	chr14:105675400-105694200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr14:105675400-105694400	Strong transcription	Brain Germinal Matrix	brain
25	chr14:105675400-105695800	Strong transcription	Dnd41	blood
26	chr14:105675600-105695400	Strong transcription	Thymus	Thymus
27	chr14:105675600-105695600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr14:105675800-105690400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr14:105675800-105693200	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr14:105676800-105713800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr14:105678400-105688800	Strong transcription	Aorta	Aorta
32	chr14:105678400-105690200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr14:105679800-105714000	Weak transcription	NHDF-Ad	bronchial
34	chr14:105680600-105688400	Strong transcription	Brain Hippocampus Middle	brain
35	chr14:105680600-105714000	Weak transcription	Psoas Muscle	Psoas
36	chr14:105681400-105687800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr14:105681400-105687800	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr14:105681400-105688000	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr14:105681400-105693200	Strong transcription	Brain Anterior Caudate	brain
40	chr14:105681400-105714000	Weak transcription	HSMMtube	muscle
41	chr14:105681400-105714200	Weak transcription	HSMM	muscle
42	chr14:105681600-105688200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr14:105681600-105688600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:105681600-105688600	Strong transcription	Brain Substantia Nigra	brain
45	chr14:105681800-105688000	Strong transcription	Brain Angular Gyrus	brain
46	chr14:105681800-105688400	Strong transcription	Brain Cingulate Gyrus	brain
47	chr14:105681800-105688600	Strong transcription	Colonic Mucosa	Colon
48	chr14:105681800-105693200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:105682200-105695800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr14:105682200-105696000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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