Variant report

Variant	rs9855516
Chromosome Location	chr3:78919319-78919320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78917237..78919813-chr3:78920275..78923386,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs72896467	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831603	0.82[AFR][1000 genomes]
rs9845857	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852334	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9858414	1.00[EUR][1000 genomes]
rs9862445	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78907600-78920200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:78916200-78923000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:78916400-78921400	Enhancers	HepG2	liver
4	chr3:78916800-78919400	Weak transcription	Brain Anterior Caudate	brain
5	chr3:78917000-78920000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:78917000-78921000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:78917400-78919400	Weak transcription	Brain Substantia Nigra	brain
8	chr3:78917400-78919600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:78917400-78919600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:78917400-78919600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:78917400-78919600	Weak transcription	A549	lung
12	chr3:78917400-78920000	Enhancers	Brain Angular Gyrus	brain
13	chr3:78917400-78920200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:78917400-78920400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:78917400-78921200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:78917400-78921200	Weak transcription	Fetal Brain Male	brain
17	chr3:78917400-78921200	Weak transcription	Fetal Kidney	kidney
18	chr3:78917400-78921400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:78917400-78927000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:78917600-78920600	Weak transcription	NH-A	brain
21	chr3:78917600-78924400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:78918000-78919400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:78918000-78919800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:78918000-78920200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:78918000-78920200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:78918000-78920200	Weak transcription	Osteobl	bone
27	chr3:78918000-78921200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:78918000-78921200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:78918000-78921400	Weak transcription	Brain Germinal Matrix	brain
30	chr3:78918000-78921400	Weak transcription	Fetal Lung	lung
31	chr3:78918000-78924800	Weak transcription	NHDF-Ad	bronchial
32	chr3:78918000-78928800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:78918000-78929800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:78918400-78919800	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:78918800-78919800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:78918800-78921000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:78918800-78921400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:78918800-78927400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:78919000-78919400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:78919200-78919800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:78919200-78920000	Enhancers	Brain Hippocampus Middle	brain
42	chr3:78919200-78923400	Enhancers	HUES48 Cell Line	embryonic stem cell

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