Variant report

Variant	rs11543540
Chromosome Location	chr3:19527405-19527406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19525585..19527422-chr3:19576707..19579689,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10510495	0.83[ASN][1000 genomes]
rs11561668	0.81[ASN][1000 genomes]
rs17005936	0.91[EUR][1000 genomes]
rs17005937	0.81[EUR][1000 genomes]
rs17005972	0.87[ASN][1000 genomes]
rs17005980	0.94[ASN][1000 genomes]
rs17005983	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17005985	0.90[EUR][1000 genomes]
rs17005998	0.91[ASN][1000 genomes]
rs17006003	0.91[ASN][1000 genomes]
rs17006010	0.95[ASN][1000 genomes]
rs17006048	0.87[ASN][1000 genomes]
rs17006054	0.83[ASN][1000 genomes]
rs17006062	0.83[ASN][1000 genomes]
rs57272811	0.81[ASN][1000 genomes]
rs57575850	0.81[EUR][1000 genomes]
rs57684768	0.92[ASN][1000 genomes]
rs58183288	0.81[EUR][1000 genomes]
rs58996643	0.83[ASN][1000 genomes]
rs60546560	0.95[ASN][1000 genomes]
rs60566663	0.83[ASN][1000 genomes]
rs60777133	0.86[ASN][1000 genomes]
rs60942804	0.95[ASN][1000 genomes]
rs61579329	0.82[ASN][1000 genomes]
rs6776448	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6781615	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6796647	0.81[EUR][1000 genomes]
rs6800537	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6801951	0.91[EUR][1000 genomes]
rs7617994	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7626734	0.83[ASN][1000 genomes]
rs7626907	0.82[ASN][1000 genomes]
rs7649671	0.82[ASN][1000 genomes]
rs7653865	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951678	0.89[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	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv948636	chr3:19335802-19856585	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv3386719	chr3:19454588-19895807	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv876595	chr3:19512074-19726308	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv3718	chr3:19520852-19565669	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19513000-19532400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:19514600-19530200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:19518000-19531600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:19518200-19535400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:19523800-19535000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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