Variant report

Variant	rs59789322
Chromosome Location	chr3:52635786-52635787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52635643..52638367-chr3:52718395..52720556,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163939	Chromatin interaction
ENSG00000163938	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17052269	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052322	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052355	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1971811	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41415947	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56815357	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57401769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57440640	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57607481	0.82[AFR][1000 genomes]
rs57931767	0.88[AFR][1000 genomes]
rs58242587	1.00[AMR][1000 genomes]
rs60351358	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60404983	1.00[AMR][1000 genomes]
rs60832323	1.00[AMR][1000 genomes]
rs61484330	1.00[AMR][1000 genomes]
rs6767229	0.85[AFR][1000 genomes]
rs6779626	0.88[AFR][1000 genomes]
rs6796577	0.91[AFR][1000 genomes]
rs6803865	0.85[AFR][1000 genomes]
rs6809065	0.91[AFR][1000 genomes]
rs7616059	0.87[AFR][1000 genomes]
rs7649820	0.88[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52621600-52635800	Weak transcription	Hela-S3	cervix
5	chr3:52627800-52640600	Weak transcription	Fetal Heart	heart
6	chr3:52628600-52640200	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr3:52630800-52638600	Strong transcription	Osteobl	bone
8	chr3:52631600-52640600	Weak transcription	Stomach Mucosa	stomach
9	chr3:52632000-52638600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:52632200-52636000	ZNF genes & repeats	Fetal Intestine Large	intestine
11	chr3:52632200-52640400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:52632400-52637200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:52633000-52636800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr3:52633000-52637200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:52633600-52635800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:52633800-52637400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:52633800-52640400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:52634000-52635800	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr3:52634000-52636000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
20	chr3:52634000-52636600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
21	chr3:52634000-52636600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
22	chr3:52634000-52636800	ZNF genes & repeats	Primary B cells from cord blood	blood
23	chr3:52634000-52636800	ZNF genes & repeats	Fetal Brain Female	brain
24	chr3:52634000-52636800	ZNF genes & repeats	Fetal Muscle Leg	muscle
25	chr3:52634000-52637000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:52634000-52637400	ZNF genes & repeats	Brain Germinal Matrix	brain
27	chr3:52634000-52637400	ZNF genes & repeats	GM12878-XiMat	blood
28	chr3:52634200-52635800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
29	chr3:52634200-52636200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
30	chr3:52634200-52636400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:52634200-52636800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:52634200-52637200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:52634200-52637400	ZNF genes & repeats	Primary T cells from cord blood	blood
34	chr3:52634200-52637600	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:52634200-52638000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:52634200-52640800	Strong transcription	HUVEC	blood vessel
37	chr3:52634200-52647800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:52634400-52636800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
39	chr3:52634400-52638200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:52634600-52635800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:52634600-52635800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:52634600-52636000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:52634600-52636000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:52634600-52636000	ZNF genes & repeats	Placenta	Placenta
45	chr3:52634600-52636000	ZNF genes & repeats	Fetal Thymus	thymus
46	chr3:52634600-52636200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
47	chr3:52634600-52636200	ZNF genes & repeats	Fetal Stomach	stomach
48	chr3:52634600-52636200	ZNF genes & repeats	HSMM	muscle
49	chr3:52634600-52636400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
50	chr3:52634600-52636400	ZNF genes & repeats	Spleen	Spleen

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