Variant report

Variant	rs12642343
Chromosome Location	chr4:141797576-141797577
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:141787778..141789643-chr4:141796789..141798752,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10519565	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12499698	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12507690	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12509724	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12640427	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12641776	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12649599	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2129645	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2220344	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4481296	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4956335	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4956488	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55761420	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55784158	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56135301	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58594074	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59222460	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60124370	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344966	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62344969	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344971	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62344995	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62344996	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62344997	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6811265	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6819107	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6829424	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6829449	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6834848	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6835056	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72722313	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9799616	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880167	chr4:141616979-142092124	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830090	chr4:141770494-141947764	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1845859	chr4:141786475-141816657	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv830091	chr4:141796603-141980546	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv275310	chr4:141797089-141797886	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv527493	chr4:141797537-141810103	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:141778400-141797600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:141778600-141798000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:141789600-141831600	Weak transcription	Aorta	Aorta
4	chr4:141792000-141797600	Weak transcription	Left Ventricle	heart
5	chr4:141792000-141797600	Weak transcription	Ovary	ovary
6	chr4:141792000-141797600	Weak transcription	Right Atrium	heart
7	chr4:141792000-141798800	Weak transcription	Right Ventricle	heart
8	chr4:141792000-141802800	Weak transcription	Gastric	stomach
9	chr4:141793800-141797600	Weak transcription	Adipose Nuclei	Adipose
10	chr4:141795200-141799000	Enhancers	Fetal Heart	heart
11	chr4:141795200-141799200	Enhancers	Fetal Lung	lung
12	chr4:141795400-141798000	Enhancers	Fetal Muscle Leg	muscle
13	chr4:141796000-141798000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:141796200-141797800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr4:141796400-141797800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:141796400-141797800	Enhancers	Brain Germinal Matrix	brain
17	chr4:141796400-141798000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:141796400-141798000	Enhancers	Fetal Brain Male	brain
19	chr4:141796400-141798200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:141796400-141798400	Enhancers	Fetal Brain Female	brain
21	chr4:141796400-141798600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:141796400-141799200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:141796600-141797800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr4:141796600-141797800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:141796800-141797600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr4:141796800-141797600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:141796800-141797600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr4:141797000-141797600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:141797000-141797600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr4:141797000-141797800	Enhancers	Brain Cingulate Gyrus	brain
31	chr4:141797000-141798000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:141797000-141798200	Enhancers	Fetal Stomach	stomach
33	chr4:141797000-141799200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:141797200-141797800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:141797200-141798600	Enhancers	Rectal Smooth Muscle	rectum
36	chr4:141797200-141798800	Enhancers	Colon Smooth Muscle	Colon
37	chr4:141797200-141799200	Enhancers	Osteobl	bone

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