Variant report

Variant	rs56959063
Chromosome Location	chr10:5500061-5500062
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	chr10:5496908..5513504-chr10:5583876..5597686,82	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10450530	1.00[AMR][1000 genomes]
rs10450531	1.00[AMR][1000 genomes]
rs4242793	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4415657	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4880730	1.00[AMR][1000 genomes]
rs56724201	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58833507	1.00[AMR][1000 genomes]
rs59584726	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59841593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60653996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60863214	0.87[AFR][1000 genomes]
rs7904871	1.00[AMR][1000 genomes]
rs7922103	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9423432	0.84[AFR][1000 genomes];1.00[AMR][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	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv932104	chr10:5203626-5641023	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv549886	chr10:5205437-5632060	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1054865	chr10:5225305-5638119	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv894797	chr10:5499173-5558349	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5489800-5508400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr10:5490200-5503800	Weak transcription	Primary B cells from cord blood	blood
3	chr10:5490400-5500200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:5490600-5507400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr10:5492600-5502400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:5493200-5502200	Strong transcription	Placenta	Placenta
7	chr10:5493400-5501000	Strong transcription	NHDF-Ad	bronchial
8	chr10:5493400-5503400	Strong transcription	NHEK	skin
9	chr10:5493400-5503800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:5493400-5503800	Weak transcription	Stomach Mucosa	stomach
11	chr10:5493600-5503000	Strong transcription	Osteobl	bone
12	chr10:5493600-5503200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:5493600-5503800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:5493800-5501000	Strong transcription	HUVEC	blood vessel
15	chr10:5493800-5501200	Strong transcription	HepG2	liver
16	chr10:5493800-5502800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:5493800-5502800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:5493800-5503000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr10:5493800-5503000	Strong transcription	NH-A	brain
20	chr10:5493800-5503200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr10:5493800-5503400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr10:5493800-5503600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:5493800-5503600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr10:5493800-5503800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:5493800-5504600	Strong transcription	A549	lung
26	chr10:5494000-5502600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr10:5494000-5502800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:5494000-5503200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:5494000-5503200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr10:5494000-5503400	Strong transcription	HSMM	muscle
31	chr10:5494200-5500600	Strong transcription	GM12878-XiMat	blood
32	chr10:5494200-5502000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:5494200-5502600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:5494200-5502800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr10:5494200-5502800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr10:5494200-5503000	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr10:5494200-5503000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:5494200-5503000	Strong transcription	Liver	Liver
39	chr10:5494400-5500600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr10:5494400-5502800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:5494400-5503000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:5494400-5503000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr10:5494400-5503000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr10:5494400-5503800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:5494600-5502200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:5494600-5503400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr10:5494600-5503600	Strong transcription	Fetal Intestine Large	intestine
48	chr10:5495000-5500200	Strong transcription	Right Ventricle	heart
49	chr10:5495000-5502600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr10:5495000-5503400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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