Variant report

Variant	rs2306576
Chromosome Location	chr15:72170686-72170687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72168681..72170784-chr15:72179926..72181699,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066933	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1074330	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs10851847	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11631650	0.81[AMR][1000 genomes]
rs11633167	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11634608	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12050794	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12148078	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12161990	0.80[AMR][1000 genomes]
rs12439494	0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898728	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898868	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902006	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs12912771	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12914070	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs12916951	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs1481860	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1481861	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1481862	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1552134	0.83[ASN][1000 genomes]
rs16956273	0.89[CEU][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap]
rs16956369	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2054601	0.83[TSI][hapmap]
rs2128112	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278987	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2306489	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2415120	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2415121	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2415126	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2415128	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28650442	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28717020	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899775	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899776	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929508	0.93[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2929509	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2929510	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2929511	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2929513	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2929517	0.88[EUR][1000 genomes]
rs2929518	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs2929525	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2929526	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2929527	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929528	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929532	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2930069	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957361	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957365	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957368	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2957373	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs2957724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957725	0.94[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2957728	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2957734	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957735	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957736	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957737	0.94[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2957740	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957742	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957745	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957746	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957750	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759820	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784310	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs3784313	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4454922	0.80[EUR][1000 genomes]
rs4511483	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4526973	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4777466	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62023343	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494973	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6494975	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6494992	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7162299	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7164780	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7172158	0.82[AMR][1000 genomes]
rs7173626	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7175373	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7177242	0.94[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7183055	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7183748	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7403191	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7496582	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7497104	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8027164	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8028115	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8030815	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8036307	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037381	0.81[EUR][1000 genomes]
rs8040216	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8178	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8557	0.94[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9302260	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs982752	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904334	chr15:71737376-72177659	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569906	chr15:72126034-72218036	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv516871	chr15:72126034-72325595	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv904336	chr15:72145937-72329906	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv569907	chr15:72154000-72215065	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv569908	chr15:72154000-72218036	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2306576	PARP6	cis	parietal	SCAN
rs2306576	SENP8	cis	cerebellum	SCAN
rs2306576	TIPIN	cis	parietal	SCAN
rs2306576	AAGAB	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72114600-72190600	Weak transcription	Pancreas	Pancrea
2	chr15:72119200-72171800	Weak transcription	Psoas Muscle	Psoas
3	chr15:72122200-72189400	Weak transcription	Right Ventricle	heart
4	chr15:72122400-72195000	Weak transcription	NHEK	skin
5	chr15:72122600-72171800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:72122600-72185200	Weak transcription	Esophagus	oesophagus
7	chr15:72122600-72195800	Weak transcription	Gastric	stomach
8	chr15:72131800-72192800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:72138200-72172400	Weak transcription	HUVEC	blood vessel
10	chr15:72140200-72171800	Weak transcription	HMEC	breast
11	chr15:72141400-72174200	Weak transcription	Fetal Brain Male	brain
12	chr15:72142600-72171800	Weak transcription	NH-A	brain
13	chr15:72142600-72183400	Weak transcription	Brain Angular Gyrus	brain
14	chr15:72142600-72189600	Weak transcription	NHLF	lung
15	chr15:72142600-72199200	Weak transcription	Hela-S3	cervix
16	chr15:72142800-72171800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:72142800-72172000	Weak transcription	Dnd41	blood
18	chr15:72142800-72176000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:72142800-72184800	Weak transcription	A549	lung
20	chr15:72142800-72190200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:72143000-72172200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:72143000-72190600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:72143000-72190600	Weak transcription	Colonic Mucosa	Colon
24	chr15:72143800-72172000	Weak transcription	Brain Germinal Matrix	brain
25	chr15:72144600-72223400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:72145400-72190600	Weak transcription	Spleen	Spleen
27	chr15:72145600-72182800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:72145600-72184800	Weak transcription	Lung	lung
29	chr15:72146200-72171800	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:72146200-72171800	Weak transcription	Left Ventricle	heart
31	chr15:72146200-72172000	Weak transcription	Brain Anterior Caudate	brain
32	chr15:72146400-72171400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:72146400-72171800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:72146400-72171800	Weak transcription	Fetal Intestine Large	intestine
35	chr15:72146400-72171800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr15:72146400-72172000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:72146400-72172200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:72146800-72171600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:72147200-72172200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr15:72149200-72186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:72151600-72171400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:72152200-72171600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:72152200-72172000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:72152600-72171600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr15:72152800-72174400	Weak transcription	HSMMtube	muscle
46	chr15:72153000-72171400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:72153000-72174600	Weak transcription	Fetal Kidney	kidney
48	chr15:72153200-72189600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:72160800-72177000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:72161000-72171800	Weak transcription	Primary T cells from cord blood	blood

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