Variant report

Variant	rs1344339
Chromosome Location	chr5:49623821-49623822
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 173 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10037889	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10038023	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10041033	0.82[ASN][1000 genomes]
rs10041903	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10042504	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10042601	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10043101	0.90[EUR][1000 genomes]
rs10051529	0.96[EUR][1000 genomes]
rs10055539	0.84[ASN][1000 genomes]
rs10056605	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10060219	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10061339	0.80[ASN][1000 genomes]
rs10062032	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10068272	0.90[ASN][1000 genomes]
rs10071725	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10072182	0.95[EUR][1000 genomes]
rs10073530	0.95[EUR][1000 genomes]
rs10074359	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10076490	0.86[ASN][1000 genomes]
rs10079493	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1010676	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs1039797	0.83[ASN][1000 genomes]
rs1039798	0.95[EUR][1000 genomes]
rs10461390	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10461391	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10461519	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10471362	0.85[ASN][1000 genomes]
rs10939999	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10940129	0.90[ASN][1000 genomes]
rs11959569	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12109228	0.90[EUR][1000 genomes]
rs12188175	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12513730	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12519021	0.85[EUR][1000 genomes]
rs12651909	0.87[ASN][1000 genomes]
rs12659303	0.93[EUR][1000 genomes]
rs12697055	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13157992	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13173678	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs13174293	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13180579	0.87[EUR][1000 genomes]
rs13180767	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13180852	0.81[ASN][1000 genomes]
rs13182357	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs13184466	0.84[EUR][1000 genomes]
rs13185587	0.85[ASN][1000 genomes]
rs13357429	0.90[CEU][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1511735	0.90[ASN][1000 genomes]
rs1511737	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1511738	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1606224	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16879094	0.81[ASN][1000 genomes]
rs1811742	1.00[CEU][hapmap]
rs1812936	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1812994	0.85[ASN][1000 genomes]
rs1833900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1995795	0.83[ASN][1000 genomes]
rs2005573	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2011539	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2011540	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2036901	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2036902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2089605	0.81[ASN][1000 genomes]
rs2137129	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2137132	0.83[ASN][1000 genomes]
rs2137134	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2199090	0.82[EUR][1000 genomes]
rs2199092	0.89[EUR][1000 genomes]
rs2271236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2352789	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2668024	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs28445612	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs28528780	0.81[ASN][1000 genomes]
rs2883164	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs303219	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs303235	0.86[ASN][1000 genomes]
rs303237	0.83[ASN][1000 genomes]
rs34185098	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34601168	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34741488	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34749302	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34945845	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35740733	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35858778	0.84[EUR][1000 genomes]
rs3849669	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3849670	0.85[ASN][1000 genomes]
rs3860731	0.86[EUR][1000 genomes]
rs3860732	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3933097	0.87[EUR][1000 genomes]
rs3950451	0.87[ASN][1000 genomes]
rs4029989	0.81[ASN][1000 genomes]
rs4030569	0.88[ASN][1000 genomes]
rs4030570	0.88[ASN][1000 genomes]
rs4030571	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4030572	0.84[ASN][1000 genomes]
rs4030573	0.88[ASN][1000 genomes]
rs4031137	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4321782	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4331898	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4337857	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4385208	0.86[EUR][1000 genomes]
rs4398636	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4495185	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4549528	0.88[ASN][1000 genomes]
rs4571473	0.82[ASN][1000 genomes]
rs4605784	0.94[EUR][1000 genomes]
rs4637546	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs471455	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs481222	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4865519	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865522	0.87[ASN][1000 genomes]
rs4865698	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4865699	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4865700	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs494540	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5011669	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs535100	0.82[EUR][1000 genomes]
rs535113	0.84[EUR][1000 genomes]
rs552892	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56104926	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs57137858	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58178891	0.93[EUR][1000 genomes]
rs58386948	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58756661	0.81[ASN][1000 genomes]
rs62365896	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62386175	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6449961	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450056	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6450063	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6450098	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6450099	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6450107	0.82[ASN][1000 genomes]
rs6450139	0.81[ASN][1000 genomes]
rs6863840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868380	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6868677	0.88[EUR][1000 genomes]
rs6868721	1.00[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap]
rs6869871	0.81[ASN][1000 genomes]
rs6871761	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874829	0.83[ASN][1000 genomes]
rs6876902	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6877713	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6897412	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7341010	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7442762	0.95[EUR][1000 genomes]
rs7442966	0.85[ASN][1000 genomes]
rs7446360	0.81[ASN][1000 genomes]
rs7446951	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7447926	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7712849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7717982	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7721808	0.85[ASN][1000 genomes]
rs7722742	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7730857	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7732000	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9291925	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9292005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760950	chr5:49432831-49624358	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1021477	chr5:49455624-49624358	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1019539	chr5:49455624-49702736	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1023402	chr5:49455624-49708458	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers 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	10 gene(s)	inside rSNPs	diseases
7	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1020912	chr5:49542837-49624358	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1344339	EMB	cis	parietal	SCAN
rs1344339	ARL15	cis	parietal	SCAN
rs1344339	EMB	cis	Whole Blood	GTEx
rs1344339	EMB	cis	Skin Sun Exposed Lower leg	GTEx
rs1344339	LOC647121	trans	multi-tissue	Pritchard
rs1344339	EMB	cis	Thyroid	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49623600-49625600	Enhancers	Primary T cells from cord blood	blood
2	chr5:49623800-49624000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:49623800-49624600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:49623800-49624600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr5:49623800-49624600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr5:49623800-49624800	Enhancers	Primary T helper cells fromperipheralblood	blood

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