Variant report

Variant	rs58582728
Chromosome Location	chr2:180138313-180138314
allele	C/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	TBP	chr2:180138176-180138734	HepG2	liver:	n/a	n/a
2	ARID3A	chr2:180138150-180138733	HepG2	liver:	n/a	chr2:180138538-180138554
3	MBD4	chr2:180136817-180138430	HepG2	liver:	n/a	n/a
4	EP300	chr2:180138300-180138617	HepG2	liver:	n/a	chr2:180138470-180138480
5	JUN	chr2:180138239-180138670	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:180137214-180138930	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180127231..180129754-chr2:180137790..180140822,6	MCF-7	breast:
2	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237477	TF binding region
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1048026	1.00[AFR][1000 genomes]
rs10497533	1.00[AFR][1000 genomes]
rs10497534	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11892241	0.84[ASN][1000 genomes]
rs11900884	0.84[ASN][1000 genomes]
rs12105478	0.81[ASN][1000 genomes]
rs16866665	0.84[ASN][1000 genomes]
rs16866673	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17363183	1.00[AFR][1000 genomes]
rs17363246	1.00[AFR][1000 genomes]
rs17363323	1.00[AFR][1000 genomes]
rs17363393	1.00[AFR][1000 genomes]
rs17363449	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17363603	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17453976	1.00[AFR][1000 genomes]
rs17454024	1.00[AFR][1000 genomes]
rs17454108	1.00[AFR][1000 genomes]
rs17454150	1.00[AFR][1000 genomes]
rs17454164	1.00[AFR][1000 genomes]
rs17454192	1.00[AFR][1000 genomes]
rs17454458	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2008215	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2028906	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2305170	1.00[AFR][1000 genomes]
rs4101465	1.00[AFR][1000 genomes]
rs4499457	1.00[AFR][1000 genomes]
rs60072979	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61179885	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6433759	0.84[ASN][1000 genomes]
rs6433766	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6725309	0.84[ASN][1000 genomes]
rs879539	1.00[AFR][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	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180130000-180141000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:180130000-180141200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:180130400-180138400	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:180130400-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:180133600-180138800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:180133600-180138800	Weak transcription	Placenta	Placenta
7	chr2:180133600-180140200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:180133800-180138800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:180133800-180138800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:180133800-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:180133800-180141200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:180134000-180139400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:180134000-180142200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:180135200-180140400	Enhancers	Brain Angular Gyrus	brain
15	chr2:180135400-180140200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:180136600-180141000	Weak transcription	Esophagus	oesophagus
17	chr2:180136800-180138800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:180137000-180139000	Flanking Active TSS	HepG2	liver
19	chr2:180137000-180139600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:180137000-180140600	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:180137200-180138600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:180137200-180138800	Enhancers	Fetal Lung	lung
23	chr2:180137200-180140000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr2:180137200-180141200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:180137200-180141200	Enhancers	Adipose Nuclei	Adipose
26	chr2:180137400-180138400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:180137400-180138600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:180137400-180138800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:180137400-180138800	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr2:180137400-180140400	Enhancers	Brain Anterior Caudate	brain
31	chr2:180137400-180141200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:180137400-180141200	Enhancers	Fetal Stomach	stomach
33	chr2:180137600-180138800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:180137600-180140600	Weak transcription	Stomach Mucosa	stomach
35	chr2:180137600-180141800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:180137800-180138400	Weak transcription	A549	lung
37	chr2:180137800-180138600	Enhancers	Fetal Muscle Leg	muscle
38	chr2:180137800-180138600	Enhancers	HMEC	breast
39	chr2:180137800-180138600	Enhancers	HSMMtube	muscle
40	chr2:180137800-180138800	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr2:180137800-180139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:180137800-180140400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:180137800-180140400	Enhancers	Osteobl	bone
44	chr2:180137800-180140600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:180138000-180138400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:180138000-180140400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:180138000-180140600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr2:180138200-180138400	Enhancers	Aorta	Aorta
49	chr2:180138200-180138400	Enhancers	Gastric	stomach
50	chr2:180138200-180138400	Enhancers	Skeletal Muscle Male	skeletal muscle

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