Variant report

Variant	rs9870509
Chromosome Location	chr3:179753966-179753967
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs9855511	0.85[AFR][1000 genomes]
rs9866196	1.00[AFR][1000 genomes]
rs9866443	0.95[AFR][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	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179726000-179754200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:179750600-179755600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:179751400-179755400	Active TSS	Brain Hippocampus Middle	brain
4	chr3:179751400-179755600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:179752200-179754000	Active TSS	Brain Substantia Nigra	brain
6	chr3:179752200-179755600	Active TSS	Brain Angular Gyrus	brain
7	chr3:179753200-179755800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:179753400-179754400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:179753400-179754800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr3:179753400-179755000	Active TSS	Dnd41	blood
11	chr3:179753400-179755200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr3:179753400-179755200	Active TSS	Brain Anterior Caudate	brain
13	chr3:179753400-179755400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr3:179753400-179755400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:179753400-179755400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:179753400-179755600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:179753400-179755600	Bivalent/Poised TSS	Fetal Brain Female	brain
18	chr3:179753600-179754000	Bivalent Enhancer	Primary T cells from cord blood	blood
19	chr3:179753600-179754000	Bivalent/Poised TSS	Fetal Brain Male	brain
20	chr3:179753600-179754000	Bivalent Enhancer	Fetal Thymus	thymus
21	chr3:179753600-179754000	Enhancers	HMEC	breast
22	chr3:179753600-179754200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr3:179753600-179754400	Flanking Active TSS	Thymus	Thymus
24	chr3:179753600-179754600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
25	chr3:179753600-179754600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
26	chr3:179753600-179755400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:179753600-179755400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:179753600-179755400	Active TSS	Pancreas	Pancrea
29	chr3:179753600-179755600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr3:179753600-179755600	Active TSS	Brain Cingulate Gyrus	brain
31	chr3:179753800-179754000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr3:179753800-179754000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr3:179753800-179754000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:179753800-179754000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
35	chr3:179753800-179754000	Active TSS	Ovary	ovary
36	chr3:179753800-179754000	Bivalent/Poised TSS	Stomach Mucosa	stomach
37	chr3:179753800-179754000	Active TSS	GM12878-XiMat	blood
38	chr3:179753800-179754200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:179753800-179754200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
40	chr3:179753800-179754200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
41	chr3:179753800-179754400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
42	chr3:179753800-179754400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:179753800-179754400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr3:179753800-179754600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:179753800-179754800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood

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