Variant report

Variant	rs2920898
Chromosome Location	chr2:55273287-55273288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
2	chr2:55131871..55133906-chr2:55272256..55273757,2	MCF-7	breast:
3	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:

Variant related genes	Relation type
ENSG00000266376	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10179594	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs12989576	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13023202	0.85[ASN][1000 genomes]
rs2580763	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2580766	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2588520	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2919125	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2920863	0.85[CHB][hapmap]
rs2920881	0.85[CHB][hapmap]
rs2920883	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2920884	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2920897	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2968789	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2968812	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2968813	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2968814	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2968829	0.85[CHB][hapmap]

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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2920898	RTN4	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
2	chr2:55259400-55275200	Weak transcription	Esophagus	oesophagus
3	chr2:55266200-55273600	Weak transcription	Primary B cells from cord blood	blood
4	chr2:55266800-55273400	Weak transcription	Fetal Thymus	thymus
5	chr2:55268000-55274800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:55270200-55274000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:55270400-55273400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:55270400-55273600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:55270600-55273400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:55271400-55275000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:55271400-55278200	Active TSS	HSMMtube	muscle
12	chr2:55271600-55273400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:55271600-55274600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:55271600-55274800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:55271600-55275000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:55271600-55275000	Weak transcription	Lung	lung
17	chr2:55271600-55275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:55271600-55275200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:55271800-55273400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:55271800-55273600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr2:55272000-55273600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr2:55272000-55274000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:55272000-55274000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:55272000-55274000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr2:55272000-55274200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:55272000-55274600	Enhancers	Rectal Smooth Muscle	rectum
27	chr2:55272000-55274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr2:55272000-55275000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:55272200-55273400	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr2:55272200-55274000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:55272200-55274600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr2:55272200-55274600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr2:55272200-55274600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:55272200-55274600	Enhancers	Fetal Lung	lung
35	chr2:55272200-55274800	Enhancers	Fetal Intestine Large	intestine
36	chr2:55272400-55273400	Flanking Active TSS	A549	lung
37	chr2:55272400-55273400	Enhancers	Hela-S3	cervix
38	chr2:55272400-55273600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:55272400-55273800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:55272400-55274400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:55272400-55274600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:55272400-55275000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:55272400-55275000	Flanking Active TSS	HUVEC	blood vessel
44	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:55272600-55273400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr2:55272600-55273400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr2:55272600-55273400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr2:55272600-55273400	Enhancers	Right Atrium	heart
49	chr2:55272600-55273800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:55272600-55273800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin

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