Variant report

Variant	rs6962389
Chromosome Location	chr7:3931746-3931747
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	chr7:3931415..3933843-chr7:3939844..3942061,2	MCF-7	breast:

Extended variants
information (count: 180 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs10085400	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10085568	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs1013880	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10215004	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs10215340	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10228397	0.90[ASN][1000 genomes]
rs10241703	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10242459	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10243770	0.90[CHB][hapmap];0.94[GIH][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10244636	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10245389	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs10246449	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs10249255	0.95[ASN][1000 genomes]
rs10250659	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10252169	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs10254099	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs10256741	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10262942	0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs10263496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10267786	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10273444	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10479833	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10479834	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10485864	0.90[ASN][1000 genomes]
rs10951315	0.82[JPT][hapmap]
rs10951322	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10951336	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10951368	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10951374	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11514766	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.93[ASN][1000 genomes]
rs11971293	0.93[ASN][1000 genomes]
rs11973090	0.89[ASN][1000 genomes]
rs11973380	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11974190	0.90[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs11974357	0.93[ASN][1000 genomes]
rs11976915	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11977993	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs11980947	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11982345	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11983563	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12112335	0.90[CHB][hapmap]
rs12531046	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531980	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs12531984	0.82[JPT][hapmap]
rs12532040	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs12532171	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.95[ASN][1000 genomes]
rs12532903	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12532912	0.80[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12533946	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12536445	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12537696	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12538997	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12539695	0.82[JPT][hapmap]
rs12540101	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12690803	0.88[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12690804	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12701219	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12701221	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12701229	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12701262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12701271	0.93[ASN][1000 genomes]
rs12701272	0.93[ASN][1000 genomes]
rs13221624	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs13236653	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs13236719	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs13245096	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1476644	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1548612	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1548613	0.82[JPT][hapmap]
rs1548614	0.82[JPT][hapmap]
rs17133859	0.84[JPT][hapmap]
rs17259867	0.82[JPT][hapmap]
rs17259924	0.82[JPT][hapmap]
rs17261199	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17325709	0.82[JPT][hapmap]
rs1962783	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1962784	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs1962785	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs2007554	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2057919	0.89[ASN][1000 genomes]
rs2057920	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2057921	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2079376	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.93[ASN][1000 genomes]
rs2079377	0.89[ASN][1000 genomes]
rs2079378	0.85[ASN][1000 genomes]
rs2097899	0.86[ASN][1000 genomes]
rs2341959	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs28491320	0.89[ASN][1000 genomes]
rs2880159	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2880204	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs28845270	0.89[ASN][1000 genomes]
rs34730154	0.90[ASN][1000 genomes]
rs41873	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4431501	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6462361	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs6462407	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6462411	0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6462412	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6462413	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6462423	0.90[ASN][1000 genomes]
rs6462447	0.95[CHD][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs6943646	0.82[JPT][hapmap]
rs6944393	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6945778	0.90[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs6948552	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6952864	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6953282	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6953604	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6953707	0.93[ASN][1000 genomes]
rs6954370	0.89[ASN][1000 genomes]
rs6955650	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6956020	0.93[ASN][1000 genomes]
rs6956479	0.90[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]
rs6957166	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6958385	0.89[ASN][1000 genomes]
rs6958535	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6959492	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6959674	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6959835	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6961230	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs6961561	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6962058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962750	0.93[ASN][1000 genomes]
rs6963058	0.89[ASN][1000 genomes]
rs6963674	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6966030	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6968148	0.89[ASN][1000 genomes]
rs6968267	0.89[ASN][1000 genomes]
rs6968272	0.89[ASN][1000 genomes]
rs6968444	0.89[ASN][1000 genomes]
rs6968948	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6969052	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6970116	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6971639	0.89[ASN][1000 genomes]
rs6971803	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6971828	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6971873	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6971953	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6972806	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6973944	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs6975313	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs6975723	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6977305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6977844	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6978060	0.89[ASN][1000 genomes]
rs6978318	0.89[ASN][1000 genomes]
rs6978964	0.90[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs6979937	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs6980085	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs768721	0.82[JPT][hapmap]
rs7778705	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7783415	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7786556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7791274	0.82[JPT][hapmap]
rs7794504	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7800775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7804166	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7807003	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7809616	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs874344	0.93[ASN][1000 genomes]
rs917168	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs917198	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs9655007	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9655343	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9655347	0.90[ASN][1000 genomes]
rs9655348	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9886069	0.92[ASN][1000 genomes]
rs9886234	0.95[ASN][1000 genomes]
rs9986911	1.00[JPT][hapmap];0.87[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	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv887336	chr7:3870810-3934909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv887337	chr7:3886254-3934909	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1019190	chr7:3896634-3943566	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1025497	chr7:3905444-4176032	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription 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	1 gene(s)	inside rSNPs	diseases
9	nsv538686	chr7:3905444-4176032	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv433014	chr7:3910039-4054769	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv1802987	chr7:3929889-3936317	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3901200-3959600	Weak transcription	Pancreas	Pancrea
2	chr7:3906800-3949000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:3923000-3940000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:3925800-3937600	Weak transcription	Spleen	Spleen
5	chr7:3926800-3936000	Weak transcription	Aorta	Aorta
6	chr7:3930600-3932800	Enhancers	Brain Germinal Matrix	brain
7	chr7:3930600-3934200	Enhancers	Fetal Brain Male	brain
8	chr7:3930800-3932800	Enhancers	Fetal Brain Female	brain
9	chr7:3931000-3932000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:3931200-3934400	Enhancers	Fetal Muscle Leg	muscle
11	chr7:3931400-3932600	Enhancers	Brain Angular Gyrus	brain
12	chr7:3931600-3932400	Enhancers	Fetal Lung	lung
13	chr7:3931600-3933000	Enhancers	Brain Hippocampus Middle	brain

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