Variant report

Variant	rs9870797
Chromosome Location	chr3:133995452-133995453
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133990638..133992986-chr3:133994149..133996265,2	MCF-7	breast:
2	chr3:133968550..133971572-chr3:133994187..133998206,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163785	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12493731	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28648514	0.88[EUR][1000 genomes]
rs3913263	1.00[JPT][hapmap]
rs4234422	0.89[EUR][1000 genomes]
rs4234423	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4234424	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs4234426	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs4470517	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs4577436	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634087	1.00[CEU][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs4682655	0.89[EUR][1000 genomes]
rs4682656	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682657	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682658	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4682665	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4682672	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854617	0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4854619	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs56104814	0.82[EUR][1000 genomes]
rs56205980	0.82[EUR][1000 genomes]
rs62271183	0.83[EUR][1000 genomes]
rs6439470	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs6439471	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439473	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439475	0.85[EUR][1000 genomes]
rs6779423	0.87[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787345	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791361	0.88[EUR][1000 genomes]
rs6795532	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs6795658	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs71807032	0.80[EUR][1000 genomes]
rs7431604	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs7433368	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7611104	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs7616326	0.88[EUR][1000 genomes]
rs7627059	0.89[EUR][1000 genomes]
rs7631521	0.82[EUR][1000 genomes]
rs7633386	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7634265	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs7646388	0.85[EUR][1000 genomes]
rs9289461	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs9812346	0.86[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9843401	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs9862959	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9883217	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs9884008	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9870797	EPHB1	cis	parietal	SCAN
rs9870797	ARMC8	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133993400-133998200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:133994000-133996200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:133994600-133996800	Enhancers	Adipose Nuclei	Adipose
4	chr3:133994600-133997200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:133994600-133997400	Enhancers	Fetal Lung	lung
6	chr3:133995000-133996800	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:133995000-133997200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:133995400-133996000	Weak transcription	Fetal Brain Male	brain
9	chr3:133995400-133996400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:133995400-133997000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:133995400-133997000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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