Variant report

Variant	rs16839647
Chromosome Location	chr3:98034684-98034685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1008191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1123188	0.81[ASN][1000 genomes]
rs11917362	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11929098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632368	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12632378	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633948	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12636571	0.84[AMR][1000 genomes]
rs12636903	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12636942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637336	0.82[AMR][1000 genomes]
rs12637340	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12637378	0.83[AMR][1000 genomes]
rs12637769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12638463	0.84[AMR][1000 genomes]
rs12638749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638827	0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12638881	0.84[AMR][1000 genomes]
rs12639159	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12639163	0.84[AMR][1000 genomes]
rs13063426	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13066249	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13066311	0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13067366	0.84[AMR][1000 genomes]
rs13067773	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13075581	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13079269	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080694	0.85[AMR][1000 genomes]
rs13086001	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088051	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13096400	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391152	0.85[AMR][1000 genomes]
rs1391156	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1497531	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1497532	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1587281	0.81[AMR][1000 genomes]
rs16839427	0.92[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs16839430	0.85[AMR][1000 genomes]
rs1874655	0.81[JPT][hapmap]
rs1964019	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1964021	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2132898	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34127316	0.83[AMR][1000 genomes]
rs34298341	0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34721537	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34829706	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35015849	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35133117	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35212708	0.85[AMR][1000 genomes]
rs35370148	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468350	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35584221	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35627913	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35807053	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36064521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3937916	0.89[ASN][1000 genomes]
rs4061832	0.89[ASN][1000 genomes]
rs4241472	0.91[CHB][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap]
rs4519740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574333	0.87[AMR][1000 genomes]
rs4603997	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4857086	0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4857363	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56220142	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59697145	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs66498739	0.85[AMR][1000 genomes]
rs6805802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71311371	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73854481	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7613182	0.89[ASN][1000 genomes]
rs7641621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872002	0.84[AMR][1000 genomes]
rs924227	0.89[ASN][1000 genomes]
rs9790053	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869347	chr3:97742604-98051633	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv877209	chr3:97806616-98049409	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv963576	chr3:97825434-98041343	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1004820	chr3:97852875-98169488	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv834773	chr3:97855362-98043888	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1000834	chr3:97859880-98095473	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv1842860	chr3:97934241-98075543	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1009918	chr3:97946030-98155450	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv34138	chr3:98034684-98045927	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98028400-98039400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:98030800-98041800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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