Variant report

Variant	rs9828213
Chromosome Location	chr3:119014342-119014343
allele	C/G
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	chr3:119013651-119014386	SK-N-SH	brain:	n/a	n/a
2	EP300	chr3:119013987-119014527	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr3:119013856-119014396	SK-N-SH_RA	brain:	n/a	chr3:119013979-119013993 chr3:119013984-119013998 chr3:119013982-119013996
4	POLR2A	chr3:119013838-119014590	SK-N-MC	brain:	n/a	n/a
5	MAX	chr3:119012573-119014384	A549	lung:	n/a	chr3:119013875-119013885
6	MXI1	chr3:119011830-119016982	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:119012572-119014343	GM18951	blood:	n/a	n/a
8	RAD21	chr3:119013726-119014380	SK-N-SH_RA	brain:	n/a	n/a
9	POLR2A	chr3:119012481-119014346	U87	brain:	n/a	n/a
10	PML	chr3:119012454-119014349	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:119012410-119014350	GM12878	blood:	n/a	n/a
12	RAD21	chr3:119013963-119014350	SK-N-SH_RA	brain:	n/a	n/a
13	POLR2A	chr3:119012253-119014459	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119011699..119014378-chr3:119015999..119019083,3	MCF-7	breast:
2	chr3:119013595..119015497-chr3:119024900..119028569,3	MCF-7	breast:
3	chr3:119012312..119014941-chr3:119040203..119043471,4	MCF-7	breast:
4	chr3:119011961..119014558-chr3:119015081..119019200,4	MCF-7	breast:
5	chr3:119011662..119015799-chr3:119040784..119043293,4	MCF-7	breast:

Variant related genes	Relation type
RPS26P21	TF binding region
ENSG00000242829	Chromatin interaction
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11917054	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11919244	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9828336	0.87[AFR][1000 genomes]
rs9830074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9830421	1.00[EUR][1000 genomes]
rs9841997	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9846150	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9860820	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119012200-119014400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:119012200-119014800	Active TSS	NHDF-Ad	bronchial
3	chr3:119012200-119015000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:119012200-119015600	Active TSS	Fetal Muscle Trunk	muscle
5	chr3:119012400-119014400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:119012400-119014400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr3:119012400-119014400	Active TSS	Sigmoid Colon	Sigmoid Colon
8	chr3:119012400-119014600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:119012400-119014800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:119012400-119014800	Active TSS	Brain Anterior Caudate	brain
11	chr3:119012400-119014800	Active TSS	Fetal Kidney	kidney
12	chr3:119012400-119015000	Active TSS	Aorta	Aorta
13	chr3:119012400-119015200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:119012400-119015200	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:119012400-119015200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:119012400-119015200	Active TSS	NHLF	lung
17	chr3:119012400-119015400	Active TSS	Fetal Intestine Small	intestine
18	chr3:119012400-119015600	Active TSS	Psoas Muscle	Psoas
19	chr3:119012400-119015800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:119012400-119015800	Active TSS	Rectal Smooth Muscle	rectum
21	chr3:119012400-119016000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:119012400-119016000	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:119012400-119016200	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr3:119012400-119016200	Active TSS	Left Ventricle	heart
25	chr3:119012400-119016200	Active TSS	Right Ventricle	heart
26	chr3:119012600-119014400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:119012600-119014400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr3:119012600-119014400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:119012600-119014400	Active TSS	Esophagus	oesophagus
30	chr3:119012600-119014400	Active TSS	A549	lung
31	chr3:119012600-119014400	Active TSS	NHEK	skin
32	chr3:119012600-119014600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr3:119012600-119014800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:119012600-119014800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr3:119012600-119014800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:119012600-119014800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:119012600-119015000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:119012600-119015000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:119012600-119015000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:119012600-119015000	Active TSS	Colon Smooth Muscle	Colon
41	chr3:119012600-119015000	Active TSS	Fetal Stomach	stomach
42	chr3:119012600-119015000	Active TSS	GM12878-XiMat	blood
43	chr3:119012600-119015200	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr3:119012600-119015200	Active TSS	Fetal Heart	heart
45	chr3:119012600-119015200	Active TSS	Stomach Smooth Muscle	stomach
46	chr3:119012600-119015400	Active TSS	Ovary	ovary
47	chr3:119012600-119015600	Active TSS	Brain Substantia Nigra	brain
48	chr3:119012600-119016000	Active TSS	Brain Hippocampus Middle	brain
49	chr3:119012600-119016000	Active TSS	Lung	lung
50	chr3:119012600-119016400	Active TSS	Pancreatic Islets	Pancreatic Islet

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