Variant report

Variant	rs6730690
Chromosome Location	chr2:20556193-20556194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20555883-20556270	MCF10A-Er-Src	breast:	n/a	n/a
2	USF1	chr2:20555838-20556216	SK-N-SH	brain:	n/a	n/a
3	FOS	chr2:20555810-20556216	MCF10A-Er-Src	breast:	n/a	n/a
4	SETDB1	chr2:20555785-20556245	U2OS	brain:	n/a	n/a
5	NFIC	chr2:20555715-20556348	SK-N-SH	brain:	n/a	chr2:20556027-20556043
6	FOS	chr2:20555809-20556248	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr2:20555807-20556216	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr2:20555814-20556268	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr2:20555821-20556243	MCF10A-Er-Src	breast:	n/a	n/a
10	TCF12	chr2:20555775-20556339	SK-N-SH	brain:	n/a	n/a
11	MYC	chr2:20555856-20556243	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20546484..20549072-chr2:20556049..20557768,2	MCF-7	breast:

Variant related genes	Relation type
PUM2	TF binding region
ENSG00000252216	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11096655	0.87[ASW][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11679966	0.91[AFR][1000 genomes]
rs11685960	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11686757	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34960190	0.83[EUR][1000 genomes]
rs4666298	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs4666299	0.84[AFR][1000 genomes]
rs4666380	0.94[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6531229	0.89[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6713329	0.94[AFR][1000 genomes]
rs7355288	0.91[AFR][1000 genomes]
rs7589798	0.89[CEU][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7596797	0.93[AFR][1000 genomes]

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20551600-20568800	Weak transcription	Psoas Muscle	Psoas
2	chr2:20552000-20556400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:20552200-20556400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:20552200-20557600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:20552200-20557600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:20552200-20562600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:20552200-20565000	Weak transcription	Esophagus	oesophagus
8	chr2:20552400-20558800	Weak transcription	Stomach Mucosa	stomach
9	chr2:20553600-20565000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:20553800-20556400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:20554000-20556200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:20554200-20562600	Weak transcription	Placenta	Placenta
13	chr2:20555000-20556400	Enhancers	HepG2	liver
14	chr2:20555200-20556400	Enhancers	NH-A	brain
15	chr2:20555200-20556800	Enhancers	HMEC	breast
16	chr2:20555400-20556800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:20555600-20556200	Enhancers	Liver	Liver
18	chr2:20555800-20556200	Enhancers	HSMM	muscle
19	chr2:20555800-20556200	Enhancers	NHDF-Ad	bronchial
20	chr2:20555800-20556400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:20555800-20556400	Enhancers	NHLF	lung
22	chr2:20555800-20556600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:20555800-20556800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:20556000-20556200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:20556000-20556200	Enhancers	Lung	lung
26	chr2:20556000-20556200	Enhancers	A549	lung
27	chr2:20556000-20556200	Enhancers	NHEK	skin
28	chr2:20556000-20556400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr2:20556000-20556400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:20556000-20556400	Enhancers	Fetal Muscle Leg	muscle
31	chr2:20556000-20556600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:20556000-20556600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:20556000-20556600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:20556000-20556600	Enhancers	GM12878-XiMat	blood
35	chr2:20556000-20556600	Enhancers	Osteobl	bone

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