Variant report

Variant	rs7975761
Chromosome Location	chr12:31545682-31545683
allele	A/G
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	CEBPB	chr12:31545484-31545719	IMR90	lung:	n/a	chr12:31545569-31545580

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31542968..31546848-chr12:31547765..31551157,4	MCF-7	breast:

Variant related genes	Relation type
RNU6-618P	TF binding region
ENSG00000200388	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1012154	0.93[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs1038066	0.81[MEX][hapmap]
rs10743757	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10743758	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap]
rs10743759	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10771827	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771828	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10771838	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10771843	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10771844	0.84[EUR][1000 genomes]
rs10771845	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10771846	0.84[EUR][1000 genomes]
rs10843942	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10843947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10843958	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843959	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843963	0.85[EUR][1000 genomes]
rs11051418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051435	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11051437	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11051439	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11051441	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1150942	0.86[CHB][hapmap]
rs1150953	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1150954	0.86[CHB][hapmap]
rs1150955	0.86[CHB][hapmap]
rs11615961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259235	0.93[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs1259236	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1259356	0.86[CHB][hapmap]
rs1259359	0.86[CHB][hapmap]
rs1259386	0.83[CHB][hapmap]
rs1259409	0.86[CHB][hapmap]
rs1259428	0.92[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs1259432	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs1259437	0.86[CHB][hapmap]
rs1272773	0.86[CHB][hapmap]
rs1469673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1677189	0.86[CHB][hapmap]
rs1716216	0.93[CHB][hapmap]
rs1996693	0.85[EUR][1000 genomes]
rs2116704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2352048	0.82[EUR][1000 genomes]
rs2374190	0.88[ASW][hapmap]
rs2568884	0.93[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs2617190	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2617191	0.86[CHB][hapmap]
rs2617200	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2682697	0.82[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2682700	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2888762	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35906870	0.80[AMR][1000 genomes]
rs3803113	0.81[EUR][1000 genomes]
rs3844573	0.89[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3850965	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs3898368	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs4482118	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs4930980	0.85[EUR][1000 genomes]
rs4931488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4931501	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4931506	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4931507	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6416254	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6487989	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6487992	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66521153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708200	0.81[AMR][1000 genomes]
rs708209	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs708214	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs708219	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7133082	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7134365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135856	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7136476	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7136943	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7137406	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71440988	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7294574	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[LWK][hapmap];1.00[MEX][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]
rs7302698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303447	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303848	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307593	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7307616	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7313118	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7313158	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7313689	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7314417	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs793146	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs793154	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793157	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs793174	0.86[CHB][hapmap]
rs793176	0.93[CHB][hapmap]
rs793177	0.86[CHB][hapmap]
rs793180	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs793184	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs793186	0.86[CHB][hapmap]
rs7954023	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7954595	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7959877	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7962896	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7963161	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7967832	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7968291	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7974437	0.88[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs7976644	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7977453	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs899159	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs9738834	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7975761	DENND5B	cis	cerebellum	SCAN
rs7975761	DENND5B	cis	parietal	SCAN
rs7975761	FLJ13224	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31535600-31560600	Weak transcription	Osteobl	bone
2	chr12:31536000-31550600	Weak transcription	Right Ventricle	heart
3	chr12:31536400-31624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:31536600-31547000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:31536600-31577400	Weak transcription	Small Intestine	intestine
6	chr12:31537200-31546400	Strong transcription	Fetal Intestine Large	intestine
7	chr12:31537200-31555600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr12:31537400-31545800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:31537400-31604800	Weak transcription	Spleen	Spleen
10	chr12:31537600-31580800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:31537800-31572400	Weak transcription	Stomach Mucosa	stomach
12	chr12:31538000-31549800	Strong transcription	A549	lung
13	chr12:31538000-31555600	Strong transcription	Liver	Liver
14	chr12:31538200-31548600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:31538400-31555000	Weak transcription	Brain Substantia Nigra	brain
16	chr12:31538600-31551600	Strong transcription	Fetal Intestine Small	intestine
17	chr12:31538600-31563400	Weak transcription	Colonic Mucosa	Colon
18	chr12:31539000-31552600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:31539400-31545800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:31539400-31546400	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:31539600-31555800	Weak transcription	NH-A	brain
22	chr12:31539800-31584800	Weak transcription	Fetal Heart	heart
23	chr12:31540000-31549400	Weak transcription	Brain Angular Gyrus	brain
24	chr12:31540400-31565200	Weak transcription	HUVEC	blood vessel
25	chr12:31540600-31549400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:31540800-31545800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:31540800-31545800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:31540800-31548600	Weak transcription	Gastric	stomach
29	chr12:31540800-31555800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:31540800-31563400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:31540800-31565400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:31540800-31572200	Weak transcription	Lung	lung
33	chr12:31540800-31573200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:31540800-31576800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:31541000-31545800	Weak transcription	NHEK	skin
36	chr12:31541000-31555800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:31542000-31578400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr12:31542200-31554000	Weak transcription	Aorta	Aorta
39	chr12:31542200-31566000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:31542200-31583600	Weak transcription	Placenta	Placenta
41	chr12:31542400-31550600	Weak transcription	HSMMtube	muscle
42	chr12:31542400-31551200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:31542400-31564600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:31542400-31565400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:31542400-31571200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:31542400-31645000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:31542600-31548000	Weak transcription	Fetal Kidney	kidney
48	chr12:31542600-31553200	Weak transcription	HepG2	liver
49	chr12:31542600-31555800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:31542600-31605800	Weak transcription	Colon Smooth Muscle	Colon

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