Variant report

Variant	rs17643347
Chromosome Location	chr4:28586794-28586795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-180C1.1.1-3	chr4:28586781-28586911	NONHSAT095913

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1024126	0.84[ASN][1000 genomes]
rs10805276	0.82[ASN][1000 genomes]
rs10805277	0.82[ASN][1000 genomes]
rs10939218	0.87[ASN][1000 genomes]
rs10939219	0.84[ASN][1000 genomes]
rs10939220	0.82[ASN][1000 genomes]
rs10939222	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11723657	0.82[ASN][1000 genomes]
rs11729559	0.82[ASN][1000 genomes]
rs11937307	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11943453	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11944357	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12331108	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12509357	0.82[ASN][1000 genomes]
rs13107472	0.82[ASN][1000 genomes]
rs13144499	0.82[ASN][1000 genomes]
rs13151535	0.82[ASN][1000 genomes]
rs16880924	0.81[ASN][1000 genomes]
rs17643041	0.87[ASN][1000 genomes]
rs17699520	0.87[ASN][1000 genomes]
rs17699721	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699827	0.87[ASN][1000 genomes]
rs17701516	0.82[ASN][1000 genomes]
rs17702089	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2309830	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2471693	0.84[ASN][1000 genomes]
rs2471694	0.84[ASN][1000 genomes]
rs2471722	0.84[ASN][1000 genomes]
rs34933409	0.82[ASN][1000 genomes]
rs35093995	0.82[ASN][1000 genomes]
rs35639254	0.82[ASN][1000 genomes]
rs4075471	0.82[ASN][1000 genomes]
rs4368591	0.82[ASN][1000 genomes]
rs4368592	0.82[ASN][1000 genomes]
rs4373152	0.82[ASN][1000 genomes]
rs4374613	0.82[ASN][1000 genomes]
rs4398515	0.82[ASN][1000 genomes]
rs4438752	0.82[ASN][1000 genomes]
rs4533764	0.82[ASN][1000 genomes]
rs4544697	0.82[ASN][1000 genomes]
rs4568230	0.82[ASN][1000 genomes]
rs4593119	0.82[ASN][1000 genomes]
rs4604048	0.82[ASN][1000 genomes]
rs4637390	0.82[ASN][1000 genomes]
rs4692331	0.82[ASN][1000 genomes]
rs4692333	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55735972	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55739909	0.81[ASN][1000 genomes]
rs57767930	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58438669	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67683753	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824212	0.82[ASN][1000 genomes]
rs6844131	0.87[ASN][1000 genomes]
rs73215429	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7656263	0.82[ASN][1000 genomes]
rs7657422	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7659143	0.82[ASN][1000 genomes]
rs7662061	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7680975	0.82[ASN][1000 genomes]
rs7682822	0.82[ASN][1000 genomes]
rs9990643	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010133	chr4:28273244-28642942	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1014938	chr4:28277683-28642942	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2757926	chr4:28543958-28839437	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759239	chr4:28543958-28839437	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv878781	chr4:28568780-28680520	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28570600-28587400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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