Variant report

Variant	rs56227556
Chromosome Location	chr5:108457593-108457594
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:40)

rs_ID	r²[population]
rs10040959	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10056058	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10063845	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10070411	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10073414	0.87[AFR][1000 genomes]
rs10085093	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10477440	0.84[AFR][1000 genomes]
rs10477944	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10477945	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10477946	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10477947	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10477948	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10477949	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10477952	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17450387	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17473391	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17534626	0.82[EUR][1000 genomes]
rs2195944	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2217649	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2416198	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2416200	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs28699553	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4957567	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4957798	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55930293	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs55953478	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57196331	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57960033	0.81[EUR][1000 genomes]
rs59337218	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6872780	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73779027	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73779047	0.81[AFR][1000 genomes]
rs73779050	0.84[AFR][1000 genomes]
rs73779051	0.82[AFR][1000 genomes]
rs73779130	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73779135	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9285864	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9326759	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9326760	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9326762	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][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	nsv830443	chr5:108326491-108496723	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv882692	chr5:108391660-108474166	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882693	chr5:108391660-108502493	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv882694	chr5:108391660-108524416	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv4953	chr5:108443905-108488747	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1027163	chr5:108445447-108839913	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv2756048	chr5:108448101-108542101	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr5:108442000-108497400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:108456800-108472800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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