Variant report

Variant	rs539039455
Chromosome Location	chr6:3987060-3987061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:3985992..3988806-chr6:4017298..4019133,2	MCF-7	breast:
2	chr6:3980920..3982632-chr6:3985928..3988379,2	MCF-7	breast:
3	chr6:3985295..3987675-chr6:3989539..3991361,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1800199	chr6:3986611-4014872	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3964800-3987400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:3976400-3990800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:3978400-3987200	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:3978600-3991000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:3978600-3991000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:3978800-3987200	Weak transcription	Fetal Stomach	stomach
7	chr6:3978800-3991000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:3978800-3991000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:3978800-3991000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:3979000-3990600	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:3979000-3990800	Weak transcription	HSMM	muscle
12	chr6:3979000-3991000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:3979000-4003200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:3979200-3990600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:3979200-3991000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:3979400-3990800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:3979800-3987200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:3980400-3987600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:3980600-3987600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:3980600-4003600	Weak transcription	Primary B cells from cord blood	blood
21	chr6:3980800-3990800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:3982200-3987400	Weak transcription	Fetal Lung	lung
23	chr6:3982400-3990600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:3983000-3987200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:3983000-3991000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr6:3983400-3987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:3983400-3987200	Weak transcription	Fetal Kidney	kidney
28	chr6:3983400-3987200	Weak transcription	Psoas Muscle	Psoas
29	chr6:3983800-3990800	Weak transcription	Ovary	ovary
30	chr6:3985000-3987200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:3985400-4011000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:3985800-3990800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:3986600-3987400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr6:3986600-3987400	Enhancers	Right Atrium	heart
35	chr6:3986600-3987600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:3986600-3987800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:3986600-3987800	Strong transcription	Primary T cells from cord blood	blood
38	chr6:3986600-3987800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr6:3986600-3987800	Enhancers	HepG2	liver
40	chr6:3986600-3988000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:3986600-3988000	Enhancers	HUVEC	blood vessel
42	chr6:3986800-3987200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:3986800-3987400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr6:3986800-3987400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:3986800-3987400	Enhancers	Small Intestine	intestine
46	chr6:3986800-3987600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:3986800-3987600	Enhancers	Placenta	Placenta
48	chr6:3986800-3987600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr6:3986800-3987800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:3986800-3987800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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