Variant report

Variant	rs539293
Chromosome Location	chr13:96749547-96749548
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96742136..96745093-chr13:96745710..96749821,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185352	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10508027	0.83[EUR][1000 genomes]
rs11616724	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11618108	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11619636	0.89[EUR][1000 genomes]
rs12428062	0.89[EUR][1000 genomes]
rs1327640	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs1330557	0.84[EUR][1000 genomes]
rs16951448	0.89[EUR][1000 genomes]
rs1788062	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1854174	0.82[AMR][1000 genomes]
rs2129006	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2170813	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2257397	0.82[AMR][1000 genomes]
rs2257398	0.84[AMR][1000 genomes]
rs2262077	0.82[AMR][1000 genomes]
rs2849439	0.87[AMR][1000 genomes]
rs4547219	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4773932	0.86[EUR][1000 genomes]
rs490753	0.86[AMR][1000 genomes]
rs492247	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492744	0.82[AMR][1000 genomes]
rs493423	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs495214	0.91[AMR][1000 genomes]
rs502311	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs504340	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs526381	0.87[AMR][1000 genomes]
rs531549	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs534010	0.87[AMR][1000 genomes]
rs534429	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs537463	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs540213	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs543775	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs544815	0.87[AMR][1000 genomes]
rs547858	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs549594	0.93[ASN][1000 genomes]
rs56077337	0.86[EUR][1000 genomes]
rs562879	0.87[AMR][1000 genomes]
rs564075	0.92[AMR][1000 genomes]
rs565297	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs565898	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs568170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs568945	0.87[AMR][1000 genomes]
rs571059	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs573909	0.82[AMR][1000 genomes]
rs581462	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs593806	1.00[ASN][1000 genomes]
rs602540	0.82[AMR][1000 genomes]
rs626317	0.84[AMR][1000 genomes]
rs627074	0.89[AMR][1000 genomes]
rs639527	0.87[AMR][1000 genomes]
rs643302	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs645595	0.91[AMR][1000 genomes]
rs647811	0.89[AMR][1000 genomes]
rs6492832	0.84[AMR][1000 genomes]
rs6492833	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6492834	0.85[AMR][1000 genomes]
rs649322	0.92[AMR][1000 genomes]
rs651812	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs672988	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs674565	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs675144	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs680576	0.89[AMR][1000 genomes]
rs680676	0.89[AMR][1000 genomes]
rs684902	0.84[AMR][1000 genomes]
rs686672	0.82[AMR][1000 genomes]
rs688133	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7139605	0.87[AMR][1000 genomes]
rs72636570	0.83[EUR][1000 genomes]
rs72637833	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72637836	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72637837	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72637840	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72638023	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72638024	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72638031	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7318247	0.82[AMR][1000 genomes]
rs7318449	0.85[AMR][1000 genomes]
rs7330650	0.85[AMR][1000 genomes]
rs7338171	0.85[AMR][1000 genomes]
rs7999737	0.84[EUR][1000 genomes]
rs816109	0.82[AMR][1000 genomes]
rs816122	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9525134	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9525136	0.84[AMR][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	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv900936	chr13:96697209-97032483	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr13:96744400-96752800	Weak transcription	Aorta	Aorta
2	chr13:96747000-96749600	Enhancers	Pancreatic Islets	Pancreatic Islet

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