Variant report

Variant	rs1320309
Chromosome Location	chr5:76171063-76171064
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	chr5:76170197..76172032-chr5:76326129..76328554,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164252	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10063816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10070865	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10462547	0.88[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs10462548	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12188004	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12519617	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs1320306	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs1320307	0.82[EUR][1000 genomes]
rs1320308	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1814969	0.95[EUR][1000 genomes]
rs2359427	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs2359658	0.83[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs55863251	0.86[EUR][1000 genomes]
rs6414971	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6869909	0.92[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs6874234	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7722773	0.82[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs9293698	0.82[EUR][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	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv3393424	chr5:76122720-76287744	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv34133	chr5:76138696-76239330	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv524024	chr5:76166018-76187777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76153000-76174400	Weak transcription	Primary T cells from cord blood	blood
2	chr5:76163800-76171800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:76165400-76171600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:76166400-76171200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:76169400-76171200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:76169400-76171400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr5:76169400-76171400	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr5:76169400-76171600	Enhancers	A549	lung
9	chr5:76169600-76171800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:76169600-76172000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr5:76169600-76172200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:76169600-76172800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:76169800-76172200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr5:76170200-76171200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr5:76170200-76172200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr5:76170400-76171200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr5:76170400-76171600	Enhancers	Primary B cells from peripheral blood	blood
18	chr5:76170600-76171200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:76170600-76171200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:76170600-76171200	Active TSS	Placenta	Placenta
21	chr5:76170600-76173400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr5:76170600-76174800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:76170800-76171200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:76170800-76172200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:76171000-76171200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr5:76171000-76171200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:76171000-76171200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr5:76171000-76171400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:76171000-76171400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
30	chr5:76171000-76171400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:76171000-76171400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr5:76171000-76171400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:76171000-76171400	Active TSS	Osteobl	bone
34	chr5:76171000-76171600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr5:76171000-76171600	Flanking Active TSS	GM12878-XiMat	blood
36	chr5:76171000-76171800	Flanking Active TSS	NH-A	brain
37	chr5:76171000-76172000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr5:76171000-76172800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:76171000-76182400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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