Variant report

Variant	rs1961940
Chromosome Location	chr3:133172446-133172447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133169398..133190840-chr3:133288286..133298861,41	MCF-7	breast:
2	chr3:133165936..133167701-chr3:133170915..133173583,2	MCF-7	breast:
3	chr3:133170643..133173658-chr3:133173707..133177209,4	MCF-7	breast:
4	chr3:133170213..133174135-chr3:133291301..133294544,7	MCF-7	breast:
5	chr3:133143999..133146404-chr3:133171252..133173491,2	MCF-7	breast:
6	chr3:133162011..133163962-chr3:133171581..133174008,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091527	Chromatin interaction
ENSG00000249993	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2078262	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2370246	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55699806	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56299019	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7632831	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][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	nsv1007047	chr3:133137664-133181388	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1006289	chr3:133137664-133186808	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1829199	chr3:133158065-133213047	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv877505	chr3:133167363-133235272	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133161000-133191000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:133165400-133178600	Weak transcription	Aorta	Aorta
3	chr3:133168200-133178800	Weak transcription	Fetal Kidney	kidney
4	chr3:133169400-133177400	Weak transcription	Thymus	Thymus
5	chr3:133169800-133179400	Weak transcription	GM12878-XiMat	blood
6	chr3:133170200-133172600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:133170200-133173200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:133170400-133177200	Weak transcription	Fetal Thymus	thymus
9	chr3:133170800-133173000	Enhancers	HepG2	liver
10	chr3:133170800-133173200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr3:133171000-133172600	Enhancers	Liver	Liver
12	chr3:133171000-133172800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:133171200-133173400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:133171400-133172600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:133171400-133172600	Enhancers	Brain Angular Gyrus	brain
16	chr3:133171400-133172600	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr3:133171800-133174600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:133172000-133172600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:133172400-133172600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:133172400-133172600	Enhancers	Placenta	Placenta
21	chr3:133172400-133172600	Enhancers	Gastric	stomach
22	chr3:133172400-133173200	Enhancers	A549	lung
23	chr3:133172400-133175600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:133172400-133178400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:133172400-133178400	Weak transcription	Stomach Mucosa	stomach

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