Variant report

Variant	rs58242587
Chromosome Location	chr3:52586837-52586838
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52586645-52586863	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:52586573-52586949	U87	brain:	n/a	n/a
3	POLR2A	chr3:52586660-52587119	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:52586573-52587005	U87	brain:	n/a	n/a
5	POLR2A	chr3:52586653-52587110	K562	blood:	n/a	n/a
6	CTCF	chr3:52586794-52586844	Kidney_OC	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52569842..52571498-chr3:52584728..52587706,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-856P	TF binding region
ENSG00000168273	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17052269	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052322	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052355	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1971811	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41415947	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56815357	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57401769	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57440640	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59078569	1.00[AFR][1000 genomes]
rs59410274	1.00[AFR][1000 genomes]
rs59789322	1.00[AMR][1000 genomes]
rs60351358	1.00[AMR][1000 genomes]
rs60404983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60832323	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61418167	1.00[AFR][1000 genomes]
rs61484330	0.98[AFR][1000 genomes];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	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
2	nsv822091	chr3:52582073-52587321	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52571400-52594200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52572400-52594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52573200-52589600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:52573200-52590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:52573400-52595000	Weak transcription	Stomach Mucosa	stomach
7	chr3:52573600-52598400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:52574200-52588400	Strong transcription	Liver	Liver
9	chr3:52574400-52623800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:52574600-52594200	Weak transcription	K562	blood
11	chr3:52574600-52598800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:52574800-52605000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:52576000-52590400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:52576800-52625600	Strong transcription	Fetal Thymus	thymus
15	chr3:52577000-52599000	Strong transcription	Fetal Muscle Leg	muscle
16	chr3:52577200-52599000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:52577600-52595400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:52577600-52598600	Strong transcription	Placenta	Placenta
19	chr3:52577600-52605200	Strong transcription	Dnd41	blood
20	chr3:52578000-52595400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:52578200-52591200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:52578200-52625600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:52578400-52588800	Strong transcription	NH-A	brain
24	chr3:52578400-52598600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:52578400-52600600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:52578600-52587000	Strong transcription	Brain Germinal Matrix	brain
27	chr3:52578800-52598200	Strong transcription	Primary B cells from cord blood	blood
28	chr3:52578800-52598800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr3:52578800-52599600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr3:52578800-52601400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:52579000-52598600	Strong transcription	Thymus	Thymus
32	chr3:52579000-52599200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:52579200-52598200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:52579400-52589600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:52580400-52589600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:52580400-52590000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:52580400-52598400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr3:52580600-52587200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:52580600-52589600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:52580600-52590800	Strong transcription	Fetal Intestine Large	intestine
41	chr3:52580600-52598400	Strong transcription	Primary T cells from cord blood	blood
42	chr3:52580600-52598600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:52580800-52588800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:52580800-52589200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:52580800-52589400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:52580800-52589800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:52580800-52598800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:52581000-52587000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:52581000-52589200	Strong transcription	Osteobl	bone
50	chr3:52581000-52589400	Strong transcription	Brain Inferior Temporal Lobe	brain

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