Variant report

Variant	rs2788106
Chromosome Location	chr9:84955250-84955251
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:84950253..84952417-chr9:84953799..84956702,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10117890	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10123309	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10125999	0.81[TSI][hapmap]
rs10780541	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10867832	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10867834	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10867835	0.82[ASN][1000 genomes]
rs10867836	0.85[ASN][1000 genomes]
rs10867837	0.83[ASN][1000 genomes]
rs10867839	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10867840	0.89[ASN][1000 genomes]
rs10867844	0.92[ASN][1000 genomes]
rs11139538	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11139554	0.90[ASN][1000 genomes]
rs11794308	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1200755	0.83[EUR][1000 genomes]
rs1327254	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1330834	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1411668	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1888327	0.95[ASN][1000 genomes]
rs1890344	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1929097	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1933577	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1933580	0.98[ASN][1000 genomes]
rs1933583	0.94[ASN][1000 genomes]
rs1933584	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1933586	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2038995	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2767709	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2774634	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2774635	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2788107	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2788109	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2788110	0.94[ASN][1000 genomes]
rs2993516	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35064221	0.92[ASN][1000 genomes]
rs3892417	0.81[CEU][hapmap]
rs4263847	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4276765	0.97[ASN][1000 genomes]
rs4338186	0.93[ASN][1000 genomes]
rs4489388	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4563967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877229	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4877691	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57058080	0.82[ASN][1000 genomes]
rs6559656	0.81[ASN][1000 genomes]
rs6559659	0.93[ASN][1000 genomes]
rs7020546	0.93[ASN][1000 genomes]
rs7021352	0.90[ASN][1000 genomes]
rs7025964	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7027988	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7848262	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7848263	0.93[ASN][1000 genomes]
rs7848823	0.94[ASN][1000 genomes]
rs7849168	0.92[ASN][1000 genomes]
rs7852603	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7857885	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7859164	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7859493	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7861490	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9410578	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893507	chr9:84799537-85097651	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893508	chr9:84954592-85080395	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893509	chr9:84954592-85097651	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893510	chr9:84954592-85117420	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:84949400-84963800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:84953600-84955600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr9:84953600-84955600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:84953800-84955400	Enhancers	Dnd41	blood
5	chr9:84954200-84955600	Enhancers	Primary hematopoietic stem cells	blood
6	chr9:84954800-84955400	Weak transcription	Fetal Lung	lung
7	chr9:84955000-84955600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:84955000-84957000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:84955200-84957000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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