Variant report

Variant	rs6823407
Chromosome Location	chr4:47502924-47502925
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:47464211..47465735-chr4:47501718..47503942,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169019	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10022723	1.00[AMR][1000 genomes]
rs10025245	1.00[AMR][1000 genomes]
rs10938489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11938614	0.81[AFR][1000 genomes]
rs4270565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4305497	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4410503	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4432727	1.00[AMR][1000 genomes]
rs4695241	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6447561	1.00[MKK][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6447563	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835123	1.00[YRI][hapmap]
rs7673088	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879005	chr4:47408838-47548254	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv829923	chr4:47436139-47678443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47488000-47533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:47488600-47514400	Weak transcription	Lung	lung
3	chr4:47488600-47524600	Weak transcription	Fetal Intestine Small	intestine
4	chr4:47488800-47559800	Weak transcription	Right Ventricle	heart
5	chr4:47489000-47512000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:47489000-47514400	Weak transcription	Fetal Stomach	stomach
7	chr4:47489000-47514600	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:47489200-47533600	Weak transcription	Esophagus	oesophagus
9	chr4:47489600-47511800	Weak transcription	HMEC	breast
10	chr4:47490000-47511800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:47490000-47512200	Weak transcription	HSMMtube	muscle
12	chr4:47490000-47514800	Weak transcription	Placenta	Placenta
13	chr4:47490200-47514200	Weak transcription	NH-A	brain
14	chr4:47492800-47514400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:47493000-47505600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:47493600-47512000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:47496000-47507200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:47496000-47512200	Weak transcription	Brain Substantia Nigra	brain
19	chr4:47496000-47514400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:47496000-47514600	Weak transcription	Ovary	ovary
21	chr4:47496200-47514400	Weak transcription	Fetal Lung	lung
22	chr4:47496400-47511800	Weak transcription	NHEK	skin
23	chr4:47500400-47503000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:47500600-47503200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr4:47500800-47503000	Enhancers	Colon Smooth Muscle	Colon
26	chr4:47500800-47503200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr4:47501000-47512400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:47501000-47527600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:47501200-47503000	Enhancers	Adipose Nuclei	Adipose
30	chr4:47501400-47503000	Enhancers	Brain Anterior Caudate	brain
31	chr4:47501400-47503000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr4:47501400-47507400	Weak transcription	Aorta	Aorta
33	chr4:47501400-47512200	Weak transcription	Liver	Liver
34	chr4:47501600-47505000	Enhancers	Primary B cells from peripheral blood	blood
35	chr4:47501800-47503000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr4:47501800-47512200	Weak transcription	HSMM	muscle
37	chr4:47502000-47503200	Enhancers	Fetal Heart	heart
38	chr4:47502200-47503000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:47502200-47503000	Enhancers	GM12878-XiMat	blood
40	chr4:47502200-47533000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:47502400-47503600	Enhancers	Primary hematopoietic stem cells	blood
42	chr4:47502400-47512000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:47502400-47512200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:47502600-47503000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:47502600-47503000	Enhancers	Left Ventricle	heart
46	chr4:47502600-47503000	Enhancers	Right Atrium	heart
47	chr4:47502600-47503000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr4:47502600-47503200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:47502600-47503200	Enhancers	Spleen	Spleen
50	chr4:47502600-47504200	Enhancers	Primary B cells from cord blood	blood

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