Variant report

Variant	rs12880291
Chromosome Location	chr14:71884567-71884568
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71869375..71872292-chr14:71882867..71885400,2	MCF-7	breast:
2	chr14:71780361..71782666-chr14:71883933..71885964,2	MCF-7	breast:

Extended variants
information (count: 184 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs10135680	0.80[EUR][1000 genomes]
rs10138557	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1029570	0.82[EUR][1000 genomes]
rs10483836	0.84[EUR][1000 genomes]
rs11627918	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs11845249	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs11848785	0.88[EUR][1000 genomes]
rs12127	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12433040	0.82[EUR][1000 genomes]
rs12878989	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12879243	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12880188	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs12880611	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12881643	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12881957	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12884929	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12885344	0.83[EUR][1000 genomes]
rs12887261	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12889866	0.90[CEU][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12891975	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12892512	0.84[EUR][1000 genomes]
rs12894016	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12894478	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12896900	0.91[CEU][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12896986	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs14030	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17178045	0.82[EUR][1000 genomes]
rs17178206	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17178234	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17178387	0.90[EUR][1000 genomes]
rs17767386	0.82[EUR][1000 genomes]
rs17767392	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs17767398	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs17767410	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs17767446	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767499	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767523	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767553	0.91[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767680	0.84[EUR][1000 genomes]
rs17767686	0.84[EUR][1000 genomes]
rs1859643	0.82[EUR][1000 genomes]
rs1981588	0.91[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1990241	0.83[EUR][1000 genomes]
rs2108049	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108057	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2108706	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs2108707	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2109276	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2190240	0.82[EUR][1000 genomes]
rs2214836	0.82[EUR][1000 genomes]
rs2332638	0.82[EUR][1000 genomes]
rs2332640	0.82[EUR][1000 genomes]
rs2332641	0.80[EUR][1000 genomes]
rs2877729	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28859432	0.80[EUR][1000 genomes]
rs33994051	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34011442	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34057981	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34061264	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34169215	0.84[EUR][1000 genomes]
rs34176710	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34281405	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34281934	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34320622	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34347034	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34388001	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34454371	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34469007	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34480562	0.84[EUR][1000 genomes]
rs34524083	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34528013	0.82[EUR][1000 genomes]
rs34528131	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34533948	0.85[EUR][1000 genomes]
rs34649709	0.84[EUR][1000 genomes]
rs34674149	0.87[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs34725136	0.85[EUR][1000 genomes]
rs34746156	0.84[EUR][1000 genomes]
rs34748537	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34767050	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34873919	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34911660	0.89[EUR][1000 genomes]
rs34957192	0.80[EUR][1000 genomes]
rs34991781	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34993988	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35051046	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35054229	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35094946	0.84[EUR][1000 genomes]
rs35122644	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35151594	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35231795	0.84[EUR][1000 genomes]
rs35260692	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35415083	0.84[EUR][1000 genomes]
rs35468256	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35589413	0.90[EUR][1000 genomes]
rs35609708	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35613269	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35620527	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35621718	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35625243	0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35680546	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35692397	0.82[EUR][1000 genomes]
rs35760654	0.84[EUR][1000 genomes]
rs35796129	0.85[EUR][1000 genomes]
rs35822724	0.86[EUR][1000 genomes]
rs35831373	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35854505	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35866366	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35971049	0.84[EUR][1000 genomes]
rs36052007	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36057816	0.82[EUR][1000 genomes]
rs36072220	0.85[EUR][1000 genomes]
rs36093218	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3784062	0.81[EUR][1000 genomes]
rs3784064	0.91[CEU][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs3784066	0.84[EUR][1000 genomes]
rs3825719	0.91[CEU][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4453405	0.90[EUR][1000 genomes]
rs4899394	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs4899398	0.91[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4902938	0.84[EUR][1000 genomes]
rs55883127	0.84[EUR][1000 genomes]
rs56180634	0.88[EUR][1000 genomes]
rs56363446	0.82[EUR][1000 genomes]
rs56407721	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989367	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989373	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989374	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989377	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989379	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61989382	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61989383	0.84[EUR][1000 genomes]
rs61989386	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61991199	0.84[EUR][1000 genomes]
rs61991200	0.90[EUR][1000 genomes]
rs61991201	0.84[EUR][1000 genomes]
rs61991202	0.85[EUR][1000 genomes]
rs61991203	0.82[EUR][1000 genomes]
rs61991204	0.82[EUR][1000 genomes]
rs61991205	0.83[EUR][1000 genomes]
rs61991213	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61991243	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61991246	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61991247	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991248	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991249	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61991250	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991254	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61991255	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6574016	0.82[EUR][1000 genomes]
rs66645707	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67489015	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68073803	0.85[EUR][1000 genomes]
rs7140354	0.82[EUR][1000 genomes]
rs7140501	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7142180	0.82[EUR][1000 genomes]
rs7142214	0.90[EUR][1000 genomes]
rs7142343	0.91[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7144299	0.82[EUR][1000 genomes]
rs7144829	0.82[EUR][1000 genomes]
rs7145755	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7147434	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7147668	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7152674	0.84[EUR][1000 genomes]
rs7152842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7154841	0.82[EUR][1000 genomes]
rs7156313	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7156460	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7157241	0.84[EUR][1000 genomes]
rs722633	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs723966	0.87[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs725673	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72728427	0.86[EUR][1000 genomes]
rs757850	0.84[EUR][1000 genomes]
rs8006300	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs8007068	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs8008605	0.82[EUR][1000 genomes]
rs8013161	0.88[EUR][1000 genomes]
rs8014349	0.82[EUR][1000 genomes]
rs8015644	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8017775	0.82[EUR][1000 genomes]
rs8019721	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9323561	0.82[EUR][1000 genomes]
rs9672060	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.84[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	nsv498021	chr14:71874708-72128721	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12880291	PCNX	cis	cerebellum	SCAN
rs12880291	MAP3K9	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71861000-71885200	Weak transcription	K562	blood
2	chr14:71866000-71889000	Weak transcription	Dnd41	blood
3	chr14:71867200-71892200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr14:71867800-71885000	Weak transcription	Brain Substantia Nigra	brain
5	chr14:71868200-71891400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr14:71869600-71904200	Weak transcription	Hela-S3	cervix
7	chr14:71870600-71891000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr14:71871600-71899600	Weak transcription	Primary B cells from cord blood	blood
9	chr14:71872600-71885000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr14:71874400-71897000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr14:71875400-71885200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:71875800-71885200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr14:71875800-71885600	Weak transcription	Brain Anterior Caudate	brain
14	chr14:71875800-71889400	Weak transcription	Fetal Kidney	kidney
15	chr14:71875800-71897400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr14:71876000-71891000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr14:71876200-71889000	Weak transcription	HSMM	muscle
18	chr14:71876200-71890800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr14:71876200-71896800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr14:71877000-71888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:71877600-71884800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr14:71877800-71888800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr14:71878200-71891000	Weak transcription	Liver	Liver
24	chr14:71878400-71891400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr14:71878600-71884600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr14:71878600-71885200	Weak transcription	Small Intestine	intestine
27	chr14:71878600-71885400	Weak transcription	Pancreas	Pancrea
28	chr14:71878600-71888600	Weak transcription	Primary T cells from cord blood	blood
29	chr14:71878600-71897200	Weak transcription	Thymus	Thymus
30	chr14:71878600-71905200	Weak transcription	Aorta	Aorta
31	chr14:71879200-71887200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr14:71881200-71899000	Weak transcription	Fetal Intestine Small	intestine
33	chr14:71882000-71884600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr14:71882000-71888400	Weak transcription	Fetal Stomach	stomach
35	chr14:71882200-71888400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:71882400-71904400	Weak transcription	NH-A	brain
37	chr14:71882800-71884800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:71882800-71887400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr14:71882800-71891200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr14:71883000-71886400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr14:71883200-71885200	Weak transcription	NHDF-Ad	bronchial
42	chr14:71883200-71887000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr14:71883400-71891000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:71883600-71884800	Weak transcription	Fetal Heart	heart
45	chr14:71883600-71886000	Strong transcription	GM12878-XiMat	blood
46	chr14:71883600-71888600	Weak transcription	Osteobl	bone
47	chr14:71883800-71884800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr14:71883800-71890200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr14:71883800-71890800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr14:71883800-71892200	Weak transcription	HMEC	breast

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