Variant report

Variant	rs2788109
Chromosome Location	chr9:84961470-84961471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10117890	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10123309	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10780541	0.89[EUR][1000 genomes]
rs10867832	0.89[EUR][1000 genomes]
rs10867834	0.90[EUR][1000 genomes]
rs10867839	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11139538	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11794308	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1200755	0.81[EUR][1000 genomes]
rs1327254	0.85[EUR][1000 genomes]
rs1330834	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1411668	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1890344	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1929097	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1933577	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1933582	0.94[ASN][1000 genomes]
rs1933584	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1933586	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2038995	0.85[EUR][1000 genomes]
rs2767709	0.83[EUR][1000 genomes]
rs2774634	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2774635	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2788106	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2788107	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2788112	0.94[ASN][1000 genomes]
rs2993516	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4263847	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4489388	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4563967	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4877231	0.92[ASN][1000 genomes]
rs4877691	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7025964	0.88[EUR][1000 genomes]
rs7027988	0.85[EUR][1000 genomes]
rs7047870	0.93[ASN][1000 genomes]
rs7848262	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7852603	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7857885	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7859164	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7859493	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7861490	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9410578	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs986510	0.81[AMR][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:4 , 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	chr9:84961000-84961800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:84961000-84962200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:84961200-84961800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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