Variant report

Variant	rs1550242
Chromosome Location	chr2:190540289-190540290
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	chr2:190540172-190540616	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190538834..190541562-chr2:190626367..190628350,2	MCF-7	breast:

Variant related genes	Relation type
ANKAR	TF binding region
ENSG00000253559	Chromatin interaction
ENSG00000128694	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1020151	1.00[AMR][1000 genomes]
rs10209441	1.00[AMR][1000 genomes]
rs10931429	1.00[AMR][1000 genomes]
rs11888722	1.00[AMR][1000 genomes]
rs1225086	1.00[AMR][1000 genomes]
rs1225103	1.00[AMR][1000 genomes]
rs12693550	1.00[AMR][1000 genomes]
rs1437880	1.00[AMR][1000 genomes]
rs1550241	1.00[AMR][1000 genomes]
rs2019099	1.00[AMR][1000 genomes]
rs2118454	1.00[AMR][1000 genomes]
rs2254040	1.00[AMR][1000 genomes]
rs2263968	1.00[AMR][1000 genomes]
rs2352288	1.00[AMR][1000 genomes]
rs5742992	1.00[AMR][1000 genomes]
rs5742999	1.00[AMR][1000 genomes]
rs5743205	1.00[AMR][1000 genomes]
rs6723158	1.00[AMR][1000 genomes]
rs893782	1.00[AMR][1000 genomes]
rs893783	1.00[AMR][1000 genomes]
rs930426	1.00[AMR][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190528200-190541600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:190530000-190542800	Strong transcription	Dnd41	blood
3	chr2:190534000-190550200	Weak transcription	K562	blood
4	chr2:190538600-190540400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:190538600-190540400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:190538800-190540400	Active TSS	NHDF-Ad	bronchial
7	chr2:190539000-190540400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:190539000-190540400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:190539000-190540400	Active TSS	A549	lung
10	chr2:190539000-190540400	Active TSS	NHLF	lung
11	chr2:190539200-190540400	Active TSS	HSMM	muscle
12	chr2:190539200-190540600	Active TSS	Hela-S3	cervix
13	chr2:190539400-190540400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:190539400-190540600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr2:190539600-190540400	Active TSS	Stomach Smooth Muscle	stomach
16	chr2:190539600-190540600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:190539600-190543400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:190539800-190540400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr2:190539800-190540400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:190539800-190540600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:190539800-190550200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:190539800-190550200	Weak transcription	Esophagus	oesophagus
23	chr2:190539800-190550200	Weak transcription	Small Intestine	intestine
24	chr2:190540000-190540400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:190540000-190540400	Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr2:190540000-190540400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:190540000-190540400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:190540000-190540400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:190540000-190540400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:190540000-190540400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:190540000-190540400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr2:190540000-190540400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr2:190540000-190540400	Enhancers	Fetal Muscle Trunk	muscle
34	chr2:190540000-190540400	Enhancers	Placenta	Placenta
35	chr2:190540000-190540400	Enhancers	Pancreas	Pancrea
36	chr2:190540000-190540400	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr2:190540000-190540400	Flanking Active TSS	HepG2	liver
38	chr2:190540000-190540400	Enhancers	NH-A	brain
39	chr2:190540000-190540600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:190540000-190540600	Active TSS	Primary T cells from cord blood	blood
41	chr2:190540000-190540600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr2:190540000-190540600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr2:190540000-190540600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:190540000-190540600	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr2:190540000-190540600	Enhancers	Fetal Heart	heart
46	chr2:190540000-190540600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr2:190540000-190540800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:190540000-190540800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:190540000-190540800	Enhancers	Lung	lung
50	chr2:190540000-190540800	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links