Variant report

Variant	rs2352262
Chromosome Location	chr2:190423785-190423786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190401323..190403546-chr2:190423221..190425184,2	MCF-7	breast:
2	chr2:190411762..190417364-chr2:190417405..190425188,8	MCF-7	breast:
3	chr2:190305157..190306928-chr2:190422807..190424459,2	MCF-7	breast:
4	chr2:190416454..190421330-chr2:190422959..190427410,6	K562	blood:
5	chr2:190420585..190423049-chr2:190423275..190425230,2	MCF-7	breast:
6	chr2:190422001..190424691-chr2:190425226..190427253,2	K562	blood:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12466208	0.87[EUR][1000 genomes]
rs12466217	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12468999	0.91[EUR][1000 genomes]
rs12478088	0.87[EUR][1000 genomes]
rs1371468	0.81[CEU][hapmap]
rs1371469	0.81[CEU][hapmap]
rs2304704	0.88[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs4145237	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs4667287	1.00[JPT][hapmap]
rs57782175	0.92[EUR][1000 genomes]
rs994226	1.00[JPT][hapmap]

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	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
2	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2352262	COL5A2	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190407400-190424200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:190413000-190424200	Weak transcription	Fetal Heart	heart
3	chr2:190414000-190424600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:190414600-190424200	Weak transcription	Dnd41	blood
5	chr2:190415200-190424200	Weak transcription	NHDF-Ad	bronchial
6	chr2:190415200-190426400	Weak transcription	HSMMtube	muscle
7	chr2:190415400-190428400	Weak transcription	HSMM	muscle
8	chr2:190416200-190425200	Enhancers	HepG2	liver
9	chr2:190417000-190431000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:190417200-190425000	Enhancers	Liver	Liver
11	chr2:190417400-190433600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:190417800-190426200	Weak transcription	K562	blood
13	chr2:190418200-190424200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:190418600-190424600	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:190418600-190425800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:190419000-190425800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:190419200-190424200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:190419800-190427800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:190419800-190428400	Weak transcription	Lung	lung
20	chr2:190420200-190425600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:190420400-190423800	Weak transcription	NHLF	lung
22	chr2:190420800-190424200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:190420800-190424200	Weak transcription	Aorta	Aorta
24	chr2:190420800-190428200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:190420800-190428400	Weak transcription	Fetal Thymus	thymus
26	chr2:190421000-190423800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:190421000-190424200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:190421000-190424200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:190421000-190424200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:190421000-190424400	Weak transcription	Right Ventricle	heart
31	chr2:190421000-190428600	Weak transcription	Fetal Brain Female	brain
32	chr2:190421000-190431000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:190421000-190431400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:190421400-190424200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:190421400-190424400	Weak transcription	Primary T cells from cord blood	blood
36	chr2:190421800-190424200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:190421800-190424400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:190422200-190424200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr2:190422400-190425400	Enhancers	Fetal Kidney	kidney
40	chr2:190422400-190426600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:190422400-190428400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:190422800-190424200	Enhancers	Adipose Nuclei	Adipose
43	chr2:190422800-190424600	Enhancers	Fetal Intestine Large	intestine
44	chr2:190422800-190424800	Enhancers	Small Intestine	intestine
45	chr2:190422800-190425000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:190422800-190425000	Enhancers	Duodenum Mucosa	Duodenum
47	chr2:190422800-190425800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:190422800-190428600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:190423200-190424200	Weak transcription	A549	lung
50	chr2:190423200-190424800	Genic enhancers	Fetal Intestine Small	intestine

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