Variant report

Variant	rs2078262
Chromosome Location	chr3:133172374-133172375
allele	A/C
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
ENSG00000249993	Chromatin interaction
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10935064	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs13069027	0.80[CHB][hapmap]
rs1881918	0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs1961940	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276737	0.86[JPT][hapmap]
rs2370246	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2737717	0.86[CHB][hapmap]
rs55699806	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56299019	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7612063	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7623519	0.81[AFR][1000 genomes]
rs7632831	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931099	0.86[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877504	chr3:133122216-133172374	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2078262	TF	cis	parietal	SCAN

Chromatin state (count:33 , 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	chr3:133167600-133172400	Weak transcription	Gastric	stomach
4	chr3:133168200-133178800	Weak transcription	Fetal Kidney	kidney
5	chr3:133169400-133177400	Weak transcription	Thymus	Thymus
6	chr3:133169800-133179400	Weak transcription	GM12878-XiMat	blood
7	chr3:133170200-133172600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:133170200-133173200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:133170400-133177200	Weak transcription	Fetal Thymus	thymus
10	chr3:133170800-133173000	Enhancers	HepG2	liver
11	chr3:133170800-133173200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:133171000-133172400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:133171000-133172400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:133171000-133172600	Enhancers	Liver	Liver
15	chr3:133171000-133172800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:133171200-133172400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:133171200-133172400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:133171200-133172400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:133171200-133172400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:133171200-133173400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:133171400-133172400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:133171400-133172400	Enhancers	Brain Hippocampus Middle	brain
23	chr3:133171400-133172600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:133171400-133172600	Enhancers	Brain Angular Gyrus	brain
25	chr3:133171400-133172600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr3:133171600-133172400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:133171600-133172400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:133171800-133174600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:133172000-133172400	Weak transcription	Placenta	Placenta
30	chr3:133172000-133172400	Enhancers	NH-A	brain
31	chr3:133172000-133172600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:133172200-133172400	Enhancers	Stomach Mucosa	stomach
33	chr3:133172200-133172400	Flanking Active TSS	A549	lung

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