Variant report

Variant	rs4888256
Chromosome Location	chr16:74607961-74607962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:74606439..74608436-chr16:74656696..74658823,2	K562	blood:
2	chr16:74607928..74610928-chr16:74610933..74614121,4	MCF-7	breast:
3	chr16:74604462..74608265-chr16:74639242..74641794,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1019572	0.84[JPT][hapmap]
rs1019573	0.84[JPT][hapmap]
rs10400930	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10500587	0.84[JPT][hapmap]
rs10871295	0.82[TSI][hapmap]
rs11149722	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs11639812	0.91[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs11644298	0.90[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs11648868	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs12325017	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs12445991	0.96[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap]
rs12446054	0.87[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap]
rs12448026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12598701	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs13339161	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs13359	0.81[CEU][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs1469140	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs1820262	0.96[CEU][hapmap]
rs2098754	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap]
rs2288053	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap]
rs2303275	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs2303278	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2303281	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs28377859	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28683674	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3785312	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs3826239	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs3923201	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4072222	0.83[CHB][hapmap];0.92[JPT][hapmap];0.85[MKK][hapmap]
rs4072450	0.81[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap]
rs4243108	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap]
rs4302071	0.81[EUR][1000 genomes]
rs4344772	0.82[EUR][1000 genomes]
rs4438331	0.90[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs4600490	0.91[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs4887772	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs4887776	0.92[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs4887777	0.92[ASW][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs4887779	0.92[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs4888238	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs4888240	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs4888242	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs4888253	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs4888255	0.94[ASN][1000 genomes]
rs4888257	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4888259	0.83[EUR][1000 genomes]
rs4888262	0.85[MKK][hapmap]
rs4888265	0.82[MKK][hapmap]
rs4888266	0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap]
rs6564117	0.83[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs6564141	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6564142	0.80[ASN][1000 genomes]
rs6564146	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6564147	0.80[ASN][1000 genomes]
rs6564148	0.81[EUR][1000 genomes]
rs6564152	0.82[ASN][1000 genomes]
rs6564153	0.82[ASN][1000 genomes]
rs6564154	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap]
rs6564157	0.91[CHB][hapmap]
rs71392603	0.86[EUR][1000 genomes]
rs7185026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7185722	0.82[ASN][1000 genomes]
rs7189123	0.91[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs7191665	0.86[MKK][hapmap]
rs7193583	0.91[YRI][hapmap]
rs7193959	0.91[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap]
rs7194143	0.90[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs7195135	0.81[EUR][1000 genomes]
rs7201105	0.82[ASN][1000 genomes]
rs7201320	0.86[MKK][hapmap]
rs7203452	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7204382	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap]
rs7204804	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.82[ASN][1000 genomes]
rs7205258	0.92[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs7342732	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap]
rs8045848	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs8047243	0.82[ASN][1000 genomes]
rs8048133	0.80[AMR][1000 genomes]
rs8048596	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8049138	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8050624	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap]
rs8050668	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8052923	0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap]
rs8053084	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8055784	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap]
rs8055803	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8056718	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8056788	0.86[AMR][1000 genomes]
rs8058034	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8058437	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8058692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8058922	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap]
rs8059869	0.92[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs8062404	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8062783	0.86[MKK][hapmap]
rs918782	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap]
rs9888968	0.82[ASN][1000 genomes]
rs9888976	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs9923145	0.85[MKK][hapmap]
rs9923616	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs9927073	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9929483	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap]
rs9930003	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9931225	0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[MKK][hapmap]
rs9932735	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9932831	0.90[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs9938833	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948443	chr16:73994997-74627711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
3	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv1060629	chr16:74483574-74660669	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv833279	chr16:74490746-74663073	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	nsv906905	chr16:74527618-74679244	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4888256	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs4888256	RFWD3	cis	Esophagus Mucosa	GTEx
rs4888256	MLKL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74563200-74622400	Weak transcription	Fetal Stomach	stomach
2	chr16:74583000-74617200	Weak transcription	Fetal Muscle Leg	muscle
3	chr16:74587600-74612200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:74588200-74623200	Weak transcription	Primary B cells from cord blood	blood
5	chr16:74589800-74626800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr16:74590200-74614600	Weak transcription	Adipose Nuclei	Adipose
7	chr16:74591000-74624000	Weak transcription	Aorta	Aorta
8	chr16:74591800-74613600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr16:74593200-74608600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr16:74595000-74622600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr16:74595800-74608400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr16:74596000-74614400	Weak transcription	Colon Smooth Muscle	Colon
13	chr16:74596200-74609400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr16:74598000-74608600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:74598200-74609200	Weak transcription	A549	lung
16	chr16:74598600-74622600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:74599000-74611000	Weak transcription	Spleen	Spleen
18	chr16:74599600-74623400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr16:74600200-74616800	Weak transcription	Fetal Kidney	kidney
20	chr16:74603400-74610800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr16:74603400-74611800	Weak transcription	NHDF-Ad	bronchial
22	chr16:74603400-74611800	Weak transcription	Osteobl	bone
23	chr16:74603600-74608000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr16:74603600-74610000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr16:74604000-74608600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr16:74605000-74609000	Weak transcription	Right Atrium	heart
27	chr16:74605000-74609200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr16:74605000-74613000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr16:74605200-74608000	Weak transcription	Fetal Heart	heart
30	chr16:74605200-74610000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr16:74605200-74612200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr16:74605200-74614000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr16:74605200-74614400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:74605200-74617000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr16:74605200-74617600	Weak transcription	Ovary	ovary
36	chr16:74605200-74630600	Weak transcription	Fetal Lung	lung
37	chr16:74605200-74639800	Weak transcription	Esophagus	oesophagus
38	chr16:74605400-74608000	Weak transcription	Brain Substantia Nigra	brain
39	chr16:74605400-74609000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr16:74605400-74611800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr16:74605400-74611800	Weak transcription	Brain Angular Gyrus	brain
42	chr16:74605400-74612000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr16:74605400-74612800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr16:74605400-74614200	Weak transcription	Thymus	Thymus
45	chr16:74605600-74630200	Weak transcription	Fetal Intestine Large	intestine
46	chr16:74606200-74609000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr16:74606200-74609400	Weak transcription	Left Ventricle	heart
48	chr16:74606400-74610200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr16:74606400-74617000	Weak transcription	Gastric	stomach
50	chr16:74606800-74608400	Enhancers	Primary T cells from cord blood	blood

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