Variant report

Variant	rs6534087
Chromosome Location	chr4:79859824-79859825
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76603369..76604011-chr4:79859804..79860621,2	Hela-S3	cervix:
2	chr4:79471198..79473938-chr4:79857809..79860687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction
ENSG00000138772	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10018189	0.90[ASN][1000 genomes]
rs10023100	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025599	0.98[ASN][1000 genomes]
rs10034295	0.90[ASN][1000 genomes]
rs11722437	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1275045	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1275046	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1275047	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13108247	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480718	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979444	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046104	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2288254	0.94[ASN][1000 genomes]
rs2554395	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822106	0.94[ASN][1000 genomes]
rs3937772	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512020	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308043	0.90[ASN][1000 genomes]
rs6534083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534086	1.00[ASN][1000 genomes]
rs6534090	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6846743	0.90[ASN][1000 genomes]
rs6854347	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688534	0.95[ASN][1000 genomes]
rs931149	0.82[ASN][1000 genomes]
rs931150	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9993426	0.82[ASN][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	nsv879504	chr4:79759796-79874275	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers 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	7 gene(s)	inside rSNPs	diseases
2	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
3	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv3392523	chr4:79859553-79862101	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79845800-79860000	Weak transcription	Small Intestine	intestine
2	chr4:79850800-79860000	Weak transcription	Gastric	stomach
3	chr4:79850800-79860000	Weak transcription	Lung	lung
4	chr4:79850800-79860000	Weak transcription	Spleen	Spleen
5	chr4:79858600-79860000	Flanking Active TSS	Dnd41	blood
6	chr4:79858800-79860200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:79859000-79860000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:79859000-79860000	Flanking Active TSS	Rectal Smooth Muscle	rectum
9	chr4:79859000-79860400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:79859000-79860800	Active TSS	GM12878-XiMat	blood
11	chr4:79859200-79860000	Enhancers	Fetal Heart	heart
12	chr4:79859200-79860200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:79859200-79860200	Flanking Active TSS	HUVEC	blood vessel
14	chr4:79859200-79861000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr4:79859200-79861000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:79859200-79861200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr4:79859200-79861200	Active TSS	NHLF	lung
18	chr4:79859200-79861400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr4:79859200-79861400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr4:79859400-79860000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:79859400-79860000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:79859400-79860000	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr4:79859400-79860000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr4:79859400-79860000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr4:79859400-79860000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:79859400-79860000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:79859400-79860000	Flanking Active TSS	HMEC	breast
28	chr4:79859400-79860800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:79859400-79860800	Active TSS	Brain Angular Gyrus	brain
30	chr4:79859400-79860800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr4:79859400-79861000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:79859400-79861000	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr4:79859400-79861000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:79859400-79861000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:79859400-79861000	Active TSS	Duodenum Mucosa	Duodenum
36	chr4:79859400-79861200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:79859400-79861200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:79859400-79861200	Active TSS	Brain Substantia Nigra	brain
39	chr4:79859400-79861200	Active TSS	Hela-S3	cervix
40	chr4:79859400-79861400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:79859400-79861400	Active TSS	Fetal Brain Female	brain
42	chr4:79859400-79861400	Active TSS	NHDF-Ad	bronchial
43	chr4:79859400-79861600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:79859400-79861600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:79859600-79860000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:79859600-79860000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:79859600-79860000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:79859600-79860000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:79859600-79860000	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr4:79859600-79860000	Flanking Active TSS	Fetal Intestine Small	intestine

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