Variant report

Variant	rs539504
Chromosome Location	chr13:91768366-91768367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:91761885..91764299-chr13:91766766..91769654,2	MCF-7	breast:
2	chr13:91766254..91768794-chr13:91789118..91791846,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1020800	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1020801	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1174782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1174784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332218	0.85[EUR][1000 genomes]
rs148771	0.85[EUR][1000 genomes]
rs167003	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16952571	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287490	0.83[ASN][1000 genomes]
rs287491	0.85[ASN][1000 genomes]
rs287494	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs287495	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs287497	0.85[ASN][1000 genomes]
rs287498	0.85[ASN][1000 genomes]
rs287500	0.82[EUR][1000 genomes]
rs287501	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287502	0.82[EUR][1000 genomes]
rs287504	0.82[EUR][1000 genomes]
rs287505	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287506	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287508	0.83[EUR][1000 genomes]
rs287509	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287510	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287511	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287512	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287513	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287514	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs287515	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287516	0.85[EUR][1000 genomes]
rs287517	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287518	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287522	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287523	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs287524	0.85[EUR][1000 genomes]
rs287525	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs287526	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287527	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs287528	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287529	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs287532	0.82[CHB][hapmap]
rs287533	0.82[CHB][hapmap]
rs3764129	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs476066	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs481037	0.85[EUR][1000 genomes]
rs492117	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502674	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504180	0.85[EUR][1000 genomes]
rs505160	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs506173	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs506238	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs512524	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs515029	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515097	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515850	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521178	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs536365	0.85[EUR][1000 genomes]
rs538062	0.85[EUR][1000 genomes]
rs543567	0.85[EUR][1000 genomes]
rs544464	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs549865	0.85[EUR][1000 genomes]
rs550731	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs558827	0.83[EUR][1000 genomes]
rs568455	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs568694	0.85[EUR][1000 genomes]
rs571202	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs582256	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs583053	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs612195	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs613553	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs620620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622426	0.85[EUR][1000 genomes]
rs623637	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs632109	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs644953	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647785	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650892	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs657464	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs665530	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684050	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs693016	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs693721	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7324853	0.85[EUR][1000 genomes]
rs76384	0.85[EUR][1000 genomes]
rs922083	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9515887	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9523257	0.87[ASN][1000 genomes]
rs9523263	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9523266	0.81[JPT][hapmap]
rs9560762	0.86[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv932206	chr13:91370888-91878374	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
4	nsv900880	chr13:91625722-91848290	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
6	nsv900881	chr13:91704312-91829940	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
8	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:91765200-91769800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:91768200-91769200	Enhancers	Fetal Kidney	kidney

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