Variant report

Variant	rs425121
Chromosome Location	chr3:78959348-78959349
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78959136..78961059-chr3:78966267..78968537,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs13075210	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162263	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162264	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162265	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162266	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162267	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs162268	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162425	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162426	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162427	0.84[EUR][1000 genomes]
rs162428	0.81[EUR][1000 genomes]
rs162429	0.83[EUR][1000 genomes]
rs186648	0.91[EUR][1000 genomes]
rs186688	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs328045	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs328047	0.90[EUR][1000 genomes]
rs329814	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329815	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs329816	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs329817	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs329818	0.90[EUR][1000 genomes]
rs329819	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs329820	0.90[EUR][1000 genomes]
rs329821	0.86[EUR][1000 genomes]
rs329822	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs329824	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329825	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs331181	0.89[EUR][1000 genomes]
rs331182	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331183	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs331184	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331188	0.83[EUR][1000 genomes]
rs331189	0.89[EUR][1000 genomes]
rs331190	0.86[EUR][1000 genomes]
rs331199	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs369346	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs379346	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs387900	0.91[EUR][1000 genomes]
rs388421	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs409361	0.86[EUR][1000 genomes]
rs420481	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs432141	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs434929	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs453354	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs479956	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs484531	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs498805	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512135	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6548601	0.82[EUR][1000 genomes]
rs6772919	0.83[EUR][1000 genomes]
rs6800782	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7617538	0.85[ASN][1000 genomes]
rs7619765	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590735	chr3:78922852-78977507	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78949200-78960600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:78956400-78962200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:78956800-78962800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:78957000-78961200	Weak transcription	A549	lung
5	chr3:78957800-78961600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:78958000-78963000	Weak transcription	HepG2	liver
7	chr3:78958400-78961400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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