Variant report

Variant	rs2872809
Chromosome Location	chr3:69338913-69338914
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	chr3:69337604..69339250-chr3:69342486..69344051,2	MCF-7	breast:
2	chr3:69337831..69342089-chr3:69345739..69348837,3	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10049245	1.00[AMR][1000 genomes]
rs10049350	1.00[AMR][1000 genomes]
rs10779991	1.00[AMR][1000 genomes]
rs1351791	1.00[AMR][1000 genomes]
rs1351792	1.00[AMR][1000 genomes]
rs2170801	1.00[AMR][1000 genomes]
rs4855378	1.00[AMR][1000 genomes]
rs4855379	1.00[AMR][1000 genomes]
rs7619331	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9310145	1.00[AMR][1000 genomes]
rs9841198	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876935	chr3:69307942-69401248	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1012483	chr3:69321191-69340525	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69293000-69343400	Weak transcription	HSMM	muscle
2	chr3:69293400-69339200	Weak transcription	Aorta	Aorta
3	chr3:69323000-69339200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:69327600-69343200	Weak transcription	Fetal Stomach	stomach
5	chr3:69328600-69339200	Weak transcription	Esophagus	oesophagus
6	chr3:69330400-69343200	Weak transcription	Fetal Thymus	thymus
7	chr3:69331400-69342200	Weak transcription	HSMMtube	muscle
8	chr3:69331600-69339400	Weak transcription	Left Ventricle	heart
9	chr3:69331600-69355400	Weak transcription	Adipose Nuclei	Adipose
10	chr3:69334600-69342800	Strong transcription	Dnd41	blood
11	chr3:69334800-69340200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:69335400-69343800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:69336400-69340400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:69336600-69340200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:69336600-69340400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:69336600-69342400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:69336800-69339600	Enhancers	Fetal Heart	heart
18	chr3:69337000-69339200	Weak transcription	Fetal Lung	lung
19	chr3:69337200-69340000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:69337200-69345400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:69337400-69339600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:69337400-69339800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:69337400-69340000	Enhancers	Brain Hippocampus Middle	brain
24	chr3:69337400-69340000	Enhancers	Brain Substantia Nigra	brain
25	chr3:69337400-69340200	Enhancers	Brain Anterior Caudate	brain
26	chr3:69337400-69344600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:69337600-69344200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:69337800-69340200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:69337800-69340200	Enhancers	Brain Cingulate Gyrus	brain
30	chr3:69338000-69339200	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:69338000-69339200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:69338000-69339200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:69338000-69339200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:69338000-69339200	Weak transcription	Spleen	Spleen
35	chr3:69338000-69339400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:69338000-69340000	Weak transcription	Fetal Brain Male	brain
37	chr3:69338000-69341200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:69338000-69341400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:69338000-69341400	Weak transcription	Placenta	Placenta
40	chr3:69338000-69343200	Weak transcription	Right Ventricle	heart
41	chr3:69338000-69343800	Weak transcription	Thymus	Thymus
42	chr3:69338200-69339200	Weak transcription	Brain Angular Gyrus	brain
43	chr3:69338200-69339200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:69338200-69339400	Weak transcription	Brain Germinal Matrix	brain
45	chr3:69338200-69339600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:69338200-69340000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
47	chr3:69338200-69340200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr3:69338200-69355800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:69338400-69339200	Weak transcription	Fetal Brain Female	brain
50	chr3:69338400-69339400	Weak transcription	H9 Cell Line	embryonic stem cell

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