Variant report

Variant	rs3789940
Chromosome Location	chr10:98085338-98085339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97802271..97805251-chr10:98083540..98085523,3	MCF-7	breast:
2	chr10:97802874..97804849-chr10:98083936..98085539,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226688	Chromatin interaction
ENSG00000107443	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10509707	0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs10786276	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10882767	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs10882773	0.88[ASW][hapmap];0.85[LWK][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs11188710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12355449	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12569756	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12573362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs17111540	0.81[JPT][hapmap]
rs1902704	0.82[JPT][hapmap]
rs1923707	0.88[ASW][hapmap];0.80[LWK][hapmap];0.81[YRI][hapmap]
rs1923708	0.81[YRI][hapmap]
rs2146385	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs2154183	0.85[YRI][hapmap]
rs2273892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2861306	0.81[JPT][hapmap]
rs3789939	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4917730	0.90[JPT][hapmap]
rs4919000	0.82[JPT][hapmap]
rs6584061	0.82[JPT][hapmap]
rs6584064	0.95[JPT][hapmap]
rs67425977	0.88[ASN][1000 genomes]
rs7072251	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs7074775	0.97[ASN][1000 genomes]
rs734225	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs734226	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7896766	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs941996	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv2761620	chr10:98047045-98089749	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831950	chr10:98080972-98245434	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98075400-98088800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr10:98077800-98089600	Strong transcription	Dnd41	blood
3	chr10:98077800-98091800	Strong transcription	Thymus	Thymus
4	chr10:98080400-98089200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:98084400-98089000	Strong transcription	Fetal Thymus	thymus
6	chr10:98085000-98086000	Enhancers	GM12878-XiMat	blood

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