Variant report

Variant	rs198852
Chromosome Location	chr6:26104448-26104449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:40)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:40 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:79826314..79826980-chr6:26103771..26104517,2	HCT-116	colon:
2	chr17:27045584..27048420-chr6:26104148..26106150,2	K562	blood:
3	chr10:74033615..74034131-chr6:26103848..26104489,2	Hela-S3	cervix:
4	chr1:163291415..163292193-chr6:26104155..26104682,2	Hela-S3	cervix:
5	chr6:26101409..26106036-chr6:27098701..27102040,8	K562	blood:
6	chr4:90032248..90033146-chr6:26103791..26104616,2	Hela-S3	cervix:
7	chr19:10654465..10655067-chr6:26103887..26104848,2	NB4	blood:
8	chr6:26103772..26104616-chr8:134308982..134309567,2	Hela-S3	cervix:
9	chr6:26104351..26106115-chr6:27801691..27803287,2	K562	blood:
10	chr6:26103055..26105911-chr6:27113369..27117045,6	K562	blood:
11	chr6:26103926..26104502-chr6:150038578..150039176,2	Hela-S3	cervix:
12	chr17:56708534..56710943-chr6:26103089..26104740,2	MCF-7	breast:
13	chr14:20937170..20938090-chr6:26103896..26104570,2	Hela-S3	cervix:
14	chr15:43622697..43623448-chr6:26103718..26104631,2	Hela-S3	cervix:
15	chr6:26104182..26105108-chr6:26204405..26205256,2	HCT-116	colon:
16	chr6:26052762..26068184-chr6:26093226..26113078,68	MCF-7	breast:
17	chr6:26042662..26045122-chr6:26102656..26104697,2	MCF-7	breast:
18	chr3:49058481..49059434-chr6:26104136..26104654,2	Hela-S3	cervix:
19	chr2:25016232..25017000-chr6:26104159..26104664,2	Hela-S3	cervix:
20	chr17:56734937..56737923-chr6:26104227..26106569,2	MCF-7	breast:
21	chr14:105957347..105957999-chr6:26104098..26104824,2	HCT-116	colon:
22	chr12:57039254..57039982-chr6:26103866..26104750,2	Hela-S3	cervix:
23	chr11:71823821..71824659-chr6:26104182..26104724,2	HCT-116	colon:
24	chr17:43249992..43250652-chr6:26104107..26104740,2	HCT-116	colon:
25	chr15:71407014..71408733-chr6:26102615..26104813,2	MCF-7	breast:
26	chr6:26103941..26105937-chr6:27113043..27115556,2	MCF-7	breast:
27	chr6:26019620..26034082-chr6:26100355..26110400,33	MCF-7	breast:
28	chr6:26104003..26105520-chr6:27859032..27861107,2	MCF-7	breast:
29	chr6:26045376..26048284-chr6:26104171..26106664,2	MCF-7	breast:
30	chr6:26104016..26104860-chr7:100026720..100027413,2	HCT-116	colon:
31	chr22:43011043..43011628-chr6:26103546..26104483,2	Hela-S3	cervix:
32	chr12:49524716..49525586-chr6:26103705..26104546,2	Hela-S3	cervix:
33	chr20:57554671..57557045-chr6:26103566..26105565,2	MCF-7	breast:
34	chr15:89877763..89878513-chr6:26104043..26104709,2	NB4	blood:
35	chr18:33709608..33710404-chr6:26103817..26104463,2	NB4	blood:
36	chr6:26104273..26104842-chr6:99968580..99969206,2	Hela-S3	cervix:
37	chr6:26103870..26104690-chr9:128003459..128004003,2	Hela-S3	cervix:
38	chr18:3601356..3603058-chr6:26104162..26105670,2	K562	blood:
39	chr17:80055762..80056584-chr6:26104111..26104952,2	HCT-116	colon:
40	chr2:190648081..190648767-chr6:26103962..26104723,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000233224	Chromatin interaction
ENSG00000198805	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000110955	Chromatin interaction
ENSG00000168806	Chromatin interaction
ENSG00000130734	Chromatin interaction
ENSG00000261441	Chromatin interaction
ENSG00000270022	Chromatin interaction
ENSG00000143248	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000110200	Chromatin interaction
ENSG00000138640	Chromatin interaction
ENSG00000138092	Chromatin interaction
ENSG00000168209	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000128699	Chromatin interaction
ENSG00000134759	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000262001	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000143228	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000198242	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000232995	Chromatin interaction
ENSG00000104419	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000225362	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000044574	Chromatin interaction
ENSG00000168803	Chromatin interaction
ENSG00000271359	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000169710	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000140521	Chromatin interaction
ENSG00000131023	Chromatin interaction
ENSG00000185347	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000101158	Chromatin interaction
ENSG00000141522	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000196226	Chromatin interaction
ENSG00000239705	Chromatin interaction
ENSG00000184924	Chromatin interaction
ENSG00000238423	Chromatin interaction
ENSG00000234816	Chromatin interaction
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10425	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs1068554	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs115810	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12346	0.80[CEU][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs129129	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs1540275	0.86[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap]
rs1540276	0.86[CHB][hapmap]
rs198801	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs198810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198818	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198834	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs198847	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs198848	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs198849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198853	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs199737	0.86[CHB][hapmap]
rs199739	0.86[CHB][hapmap]
rs199741	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs199750	0.96[CHD][hapmap];0.83[GIH][hapmap]
rs199751	0.86[CHB][hapmap]
rs199752	0.96[CHD][hapmap]
rs199753	0.86[CHB][hapmap]
rs199754	0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap]
rs2032447	0.88[CHD][hapmap];0.84[GIH][hapmap]
rs2213284	0.96[CHD][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap]
rs2230655	0.86[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap]
rs4401650	0.92[CHD][hapmap];0.86[GIH][hapmap]
rs442601	0.86[CHB][hapmap]
rs6901039	0.86[CHB][hapmap];0.96[CHD][hapmap]
rs6922788	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs7756117	0.92[CHD][hapmap];0.84[GIH][hapmap]
rs807212	0.86[CHB][hapmap]
rs807214	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
8	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
9	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
10	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
11	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
12	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
13	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
14	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
15	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
16	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
17	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
18	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs198852	BTN2A2	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26103200-26104800	Flanking Active TSS	NHEK	skin
2	chr6:26103200-26105000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:26103400-26104600	Active TSS	Thymus	Thymus
4	chr6:26103400-26104800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:26103400-26104800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:26103400-26104800	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr6:26103400-26104800	Flanking Active TSS	HUVEC	blood vessel
8	chr6:26103400-26104800	Active TSS	NHDF-Ad	bronchial
9	chr6:26103400-26105000	Active TSS	NHLF	lung
10	chr6:26103400-26105200	Active TSS	A549	lung
11	chr6:26103600-26104600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:26103600-26104600	Active TSS	Brain Cingulate Gyrus	brain
13	chr6:26103600-26104600	Active TSS	Brain Hippocampus Middle	brain
14	chr6:26103600-26104600	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr6:26103600-26104600	Active TSS	Colon Smooth Muscle	Colon
16	chr6:26103600-26104600	Active TSS	Right Ventricle	heart
17	chr6:26103600-26104800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:26103600-26104800	Active TSS	Brain Anterior Caudate	brain
19	chr6:26103600-26104800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:26103600-26104800	Active TSS	Fetal Brain Male	brain
21	chr6:26103600-26104800	Active TSS	Psoas Muscle	Psoas
22	chr6:26103600-26104800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr6:26103600-26105000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:26103600-26105000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:26103600-26105000	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr6:26103600-26105000	Active TSS	Fetal Brain Female	brain
27	chr6:26103600-26105000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr6:26103600-26105000	Active TSS	Stomach Smooth Muscle	stomach
29	chr6:26103600-26105000	Active TSS	Hela-S3	cervix
30	chr6:26103600-26105200	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr6:26103600-26105200	Active TSS	Colonic Mucosa	Colon
32	chr6:26103800-26104600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:26103800-26104600	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr6:26103800-26104600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:26103800-26104600	Active TSS	Liver	Liver
36	chr6:26103800-26104600	Active TSS	Brain Angular Gyrus	brain
37	chr6:26103800-26104600	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr6:26103800-26104600	Active TSS	NH-A	brain
39	chr6:26103800-26104800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:26103800-26104800	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr6:26103800-26104800	Active TSS	Brain Germinal Matrix	brain
42	chr6:26103800-26104800	Active TSS	Brain Substantia Nigra	brain
43	chr6:26103800-26104800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr6:26103800-26104800	Active TSS	Fetal Lung	lung
45	chr6:26103800-26105000	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr6:26103800-26105000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:26103800-26105000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:26103800-26105000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:26103800-26105000	Active TSS	Rectal Smooth Muscle	rectum
50	chr6:26103800-26105000	Active TSS	GM12878-XiMat	blood

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