Variant report

Variant	rs12272795
Chromosome Location	chr11:46544072-46544073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46529319..46531334-chr11:46543160..46545950,2	MCF-7	breast:
2	chr11:46543133..46545904-chr11:46548036..46550406,2	K562	blood:
3	chr11:46410960..46411481-chr11:46544032..46544713,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10160701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838602	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11038897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11038900	0.94[EUR][1000 genomes]
rs11038906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11038914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11038919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11038927	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11819869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12283172	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12292425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12295266	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12573978	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12574250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12574259	0.93[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs12574668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs12575519	0.90[EUR][1000 genomes]
rs12576115	0.88[EUR][1000 genomes]
rs12576317	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12576359	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12577142	0.89[EUR][1000 genomes]
rs12578042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1472001	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1489192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16938506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17197116	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2046768	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs2067482	0.92[EUR][1000 genomes]
rs2171667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2171668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279465	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs2291487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2864072	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2864076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2902858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34406563	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs35623865	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3740974	0.92[EUR][1000 genomes]
rs3740977	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs3802888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809047	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs4307676	0.83[EUR][1000 genomes]
rs4319473	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs55657382	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55661562	0.87[EUR][1000 genomes]
rs55750336	0.86[ASN][1000 genomes]
rs57535407	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58147945	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59319338	0.89[EUR][1000 genomes]
rs60722866	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60932698	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61882678	0.84[EUR][1000 genomes]
rs61882682	0.90[EUR][1000 genomes]
rs61882683	0.87[EUR][1000 genomes]
rs61882691	0.90[EUR][1000 genomes]
rs61882701	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882702	0.92[EUR][1000 genomes]
rs61882706	0.91[EUR][1000 genomes]
rs61882709	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61882710	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61882711	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61882712	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61882720	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61882743	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61882746	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61882748	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61882750	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61882756	0.87[EUR][1000 genomes]
rs61882757	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61882758	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61884262	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61884264	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61884271	0.85[EUR][1000 genomes]
rs61884273	0.83[EUR][1000 genomes]
rs61884274	0.83[EUR][1000 genomes]
rs6485682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6485685	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7108770	0.83[EUR][1000 genomes]
rs7109698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs7112229	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7122039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7125907	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7126316	0.82[EUR][1000 genomes]
rs7126343	0.83[EUR][1000 genomes]
rs7127529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7128092	0.82[EUR][1000 genomes]
rs7130141	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73449983	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7481312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7484002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs756343	0.86[ASN][1000 genomes]
rs7924401	0.86[EUR][1000 genomes]
rs7926389	0.93[CEU][hapmap]
rs7930103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7932866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7936413	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs7946705	0.92[EUR][1000 genomes]
rs7951579	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7951870	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs876701	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];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	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046990	chr11:46501436-46669636	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv541031	chr11:46501436-46669636	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv897321	chr11:46515902-46673344	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12272795	ATG13	cis	parietal	SCAN
rs12272795	C11orf49	cis	parietal	SCAN
rs12272795	DKFZp779M0652	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46503400-46563000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:46517200-46550000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr11:46530200-46544200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:46530200-46550200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:46530200-46550600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:46530400-46544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr11:46530400-46550400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:46530400-46550600	Weak transcription	Spleen	Spleen
9	chr11:46530400-46556000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:46530400-46559000	Weak transcription	Fetal Thymus	thymus
11	chr11:46530400-46561800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:46530600-46550800	Weak transcription	Colonic Mucosa	Colon
13	chr11:46534400-46550400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:46534400-46550600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:46534800-46544600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:46535200-46550600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr11:46535600-46563200	Weak transcription	Small Intestine	intestine
18	chr11:46535800-46549200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:46535800-46550800	Weak transcription	Lung	lung
20	chr11:46535800-46563200	Weak transcription	Pancreas	Pancrea
21	chr11:46536000-46544400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:46536000-46544400	Weak transcription	Stomach Mucosa	stomach
23	chr11:46536000-46544600	Weak transcription	Fetal Brain Female	brain
24	chr11:46536000-46550400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr11:46536000-46563200	Weak transcription	Fetal Stomach	stomach
26	chr11:46536200-46550800	Weak transcription	K562	blood
27	chr11:46536400-46544200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:46536400-46550600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:46536800-46544600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:46536800-46548200	Weak transcription	Primary B cells from cord blood	blood
31	chr11:46536800-46551400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:46538600-46544400	Weak transcription	A549	lung
33	chr11:46538600-46550600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr11:46538600-46550800	Weak transcription	Dnd41	blood
35	chr11:46538600-46559400	Weak transcription	Thymus	Thymus
36	chr11:46539600-46544800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr11:46539600-46545200	Enhancers	Liver	Liver
38	chr11:46541200-46549200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:46541200-46549800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr11:46541200-46550400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr11:46541400-46550800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:46541400-46563200	Weak transcription	Aorta	Aorta
43	chr11:46541800-46544200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:46541800-46545400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr11:46542000-46545000	Enhancers	Brain Substantia Nigra	brain
46	chr11:46542400-46544400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:46542400-46544800	Enhancers	HSMMtube	muscle
48	chr11:46542600-46544200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr11:46542600-46544600	Enhancers	HSMM	muscle
50	chr11:46542600-46544800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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