Variant report

Variant	rs17052501
Chromosome Location	chr3:52858621-52858622
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52857160..52859270-chr3:52860269..52862799,2	K562	blood:
2	chr3:52834279..52837211-chr3:52858122..52860407,2	K562	blood:

Variant related genes	Relation type
ENSG00000162267	Chromatin interaction
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17052546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052577	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1986467	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34967967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35672271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3774362	1.00[AFR][1000 genomes]
rs58562470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58763303	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv590308	chr3:52854335-52860806	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv876798	chr3:52856609-52863133	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52846400-52860800	Weak transcription	Esophagus	oesophagus
2	chr3:52847200-52861200	Genic enhancers	Liver	Liver
3	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
4	chr3:52848400-52865800	Weak transcription	Ovary	ovary
5	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
6	chr3:52850600-52864200	Strong transcription	Stomach Smooth Muscle	stomach
7	chr3:52850800-52865400	Strong transcription	Fetal Stomach	stomach
8	chr3:52851600-52863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
11	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:52853200-52859400	Strong transcription	Thymus	Thymus
13	chr3:52853400-52861200	Strong transcription	Fetal Muscle Leg	muscle
14	chr3:52854000-52858800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:52854000-52859000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:52854000-52861200	Strong transcription	Pancreas	Pancrea
17	chr3:52854200-52859000	Strong transcription	Brain Cingulate Gyrus	brain
18	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:52854400-52861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:52855000-52861600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:52855200-52860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:52855200-52865400	Weak transcription	Brain Substantia Nigra	brain
25	chr3:52855600-52862000	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:52855600-52865400	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:52856000-52865400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
29	chr3:52856200-52859000	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr3:52856200-52865600	Weak transcription	Left Ventricle	heart
31	chr3:52856400-52868200	Weak transcription	Fetal Lung	lung
32	chr3:52856600-52859200	Strong transcription	Brain Anterior Caudate	brain
33	chr3:52856600-52860400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:52856600-52861000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr3:52856600-52861200	Strong transcription	Primary T cells from cord blood	blood
36	chr3:52856600-52864400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:52856800-52859000	Strong transcription	Lung	lung
38	chr3:52856800-52859400	Strong transcription	Fetal Intestine Small	intestine
39	chr3:52856800-52863400	Strong transcription	Fetal Thymus	thymus
40	chr3:52857000-52858800	Strong transcription	Aorta	Aorta
41	chr3:52857000-52861000	Weak transcription	HepG2	liver
42	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:52857200-52858800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:52857400-52858800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:52857800-52865400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:52858000-52858800	Enhancers	Placenta	Placenta
47	chr3:52858000-52867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:52858000-52868400	Weak transcription	Brain Germinal Matrix	brain
49	chr3:52858200-52865400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:52858400-52861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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