Variant report

Variant	rs10936173
Chromosome Location	chr3:158906650-158906651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10470473	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10513537	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10936175	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs10936176	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs11715082	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs11924990	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs13326945	1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs1449021	0.84[EUR][1000 genomes]
rs17727250	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1823311	0.81[CHB][hapmap]
rs1868414	0.81[CHB][hapmap]
rs2122147	0.80[EUR][1000 genomes]
rs2365483	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2365490	0.87[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs3924807	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4679855	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680492	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4680497	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680498	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57473274	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58290749	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6441253	0.81[CHB][hapmap]
rs6777541	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs6781221	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs6791853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs9283610	0.81[CHB][hapmap]
rs9820047	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs9821641	0.81[CHB][hapmap]
rs9827242	1.00[CEU][hapmap]
rs9827400	0.89[CEU][hapmap]
rs9829189	0.84[EUR][1000 genomes]
rs9831067	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs9834328	0.81[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs9838646	1.00[ASW][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap]
rs9839112	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs9840972	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9852196	0.81[EUR][1000 genomes]
rs9856166	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9862769	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap]
rs9878883	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9880642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS 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 miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3426016	chr3:158676623-158979242	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv491927	chr3:158692653-158952780	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158899600-158907400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:158903200-158909200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:158905000-158907400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:158905600-158907600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:158906000-158907600	Enhancers	Liver	Liver
6	chr3:158906600-158909200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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