Variant report

Variant	rs1399913
Chromosome Location	chr3:161375580-161375581
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	chr3:161373878..161376279-chr3:161388444..161390253,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1106255	0.89[AFR][1000 genomes]
rs1399906	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399908	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399909	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399910	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399915	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1399916	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1515725	0.91[AFR][1000 genomes]
rs1515741	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1515743	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1568020	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1588908	0.90[AFR][1000 genomes]
rs16832928	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1849999	0.96[ASN][1000 genomes]
rs1850000	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1878064	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2203490	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2222055	0.91[AFR][1000 genomes]
rs4305435	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4472057	0.91[AFR][1000 genomes]
rs4856709	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4856712	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441393	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441395	0.91[AFR][1000 genomes]
rs6809783	0.91[AFR][1000 genomes]
rs7620901	0.87[ASN][1000 genomes]
rs7629214	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7652034	0.91[AFR][1000 genomes]
rs9290088	0.96[ASN][1000 genomes]
rs9820806	0.91[AFR][1000 genomes]
rs9829196	0.91[AFR][1000 genomes]
rs9859298	0.85[ASN][1000 genomes]
rs9867300	0.91[AFR][1000 genomes]
rs9871565	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872386	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876363	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876608	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9877938	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9879265	0.96[ASN][1000 genomes]
rs9879283	0.85[AFR][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	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
2	nsv829774	chr3:161229405-161386919	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2422309	chr3:161242389-161425932	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv877711	chr3:161275848-161486665	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1004255	chr3:161340249-161476537	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 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	chr3:161374800-161376000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr3:161375400-161378400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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