Variant report

Variant	rs1562787
Chromosome Location	chr3:150087238-150087239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150068040..150070042-chr3:150085937..150088892,3	MCF-7	breast:
2	chr3:150086902..150089689-chr3:150137707..150139758,2	MCF-7	breast:
3	chr3:150086313..150087997-chr3:150093926..150095671,2	MCF-7	breast:
4	chr3:150081211..150094856-chr3:150124384..150132921,41	MCF-7	breast:
5	chr3:150086685..150087637-chr3:150126106..150126862,2	MCF-7	breast:
6	chr3:150081035..150094397-chr3:150122156..150134666,40	MCF-7	breast:
7	chr3:150086784..150089218-chr3:150089694..150091385,2	MCF-7	breast:
8	chr3:150081232..150084545-chr3:150085072..150089813,5	K562	blood:
9	chr3:150086785..150088735-chr3:150127952..150130742,2	K562	blood:
10	chr3:150031134..150033723-chr3:150086992..150089751,2	MCF-7	breast:
11	chr3:150010377..150012973-chr3:150087028..150089322,2	MCF-7	breast:
12	chr3:150086519..150091866-chr3:150093461..150097312,5	K562	blood:
13	chr3:149953883..149958002-chr3:150086576..150089576,4	MCF-7	breast:
14	chr3:150061806..150067641-chr3:150085085..150089827,11	MCF-7	breast:
15	chr3:149954498..149958099-chr3:150086943..150091403,7	MCF-7	breast:
16	chr3:150086925..150089531-chr3:150177059..150179337,2	K562	blood:
17	chr3:150087084..150094553-chr3:150124263..150130094,16	K562	blood:
18	chr3:150086378..150089997-chr3:150256465..150259602,3	MCF-7	breast:
19	chr3:150033113..150037399-chr3:150086580..150091176,6	MCF-7	breast:
20	chr3:150081232..150084840-chr3:150085072..150088254,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196428	Chromatin interaction
ENSG00000244541	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10154963	0.83[ASN][1000 genomes]
rs10804747	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066779	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1376025	0.80[ASN][1000 genomes]
rs1450341	0.84[ASN][1000 genomes]
rs1450343	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1463229	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1466131	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562789	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2903834	0.81[JPT][hapmap]
rs4323025	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4681202	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs6414375	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6763422	0.82[ASN][1000 genomes]
rs6778948	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7430585	0.86[ASN][1000 genomes]
rs7642773	0.95[JPT][hapmap]
rs9844184	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9855441	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9881867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][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	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150081200-150088200	Weak transcription	Stomach Mucosa	stomach
2	chr3:150082400-150089400	Weak transcription	HepG2	liver
3	chr3:150083200-150088000	Weak transcription	Esophagus	oesophagus
4	chr3:150083200-150088200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:150083200-150088200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:150083800-150087400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:150083800-150087400	Weak transcription	NH-A	brain
8	chr3:150084000-150087800	Weak transcription	HSMM	muscle
9	chr3:150084600-150087800	Weak transcription	Fetal Kidney	kidney
10	chr3:150084600-150088000	Weak transcription	Right Atrium	heart
11	chr3:150085000-150087600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:150085200-150087800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:150085200-150088000	Enhancers	Hela-S3	cervix
14	chr3:150085400-150088000	Enhancers	NHDF-Ad	bronchial
15	chr3:150085600-150087400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:150085600-150088000	Enhancers	Osteobl	bone
17	chr3:150085800-150088800	Enhancers	Placenta	Placenta
18	chr3:150086000-150087400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:150086000-150087600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:150086000-150087800	Weak transcription	Fetal Lung	lung
21	chr3:150086200-150087800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:150086200-150102200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:150086400-150087600	Enhancers	A549	lung
24	chr3:150086600-150087600	Enhancers	HUVEC	blood vessel
25	chr3:150086600-150087800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:150086600-150087800	Enhancers	NHEK	skin
27	chr3:150086600-150088000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:150086600-150088000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:150086800-150087400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:150086800-150087800	Enhancers	HMEC	breast
31	chr3:150086800-150088000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:150087000-150087600	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:150087000-150087600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:150087000-150087800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:150087000-150088000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:150087000-150088000	Weak transcription	NHLF	lung
37	chr3:150087000-150088200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr3:150087200-150087600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:150087200-150087600	Enhancers	HSMMtube	muscle
40	chr3:150087200-150087800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:150087200-150087800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:150087200-150087800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:150087200-150088200	Weak transcription	K562	blood
44	chr3:150087200-150089000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:150087200-150089200	Enhancers	Fetal Muscle Leg	muscle

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