Variant report

Variant	rs12500124
Chromosome Location	chr4:86729172-86729173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86728075..86730663-chr4:86957838..86959662,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12499386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503243	0.81[TSI][hapmap]
rs12504839	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504871	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512001	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17010960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17011016	0.82[CEU][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs17011065	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs17011069	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs345364	0.82[CEU][hapmap]
rs345365	0.82[CEU][hapmap]
rs345370	0.82[CEU][hapmap]
rs4693742	0.82[ASN][1000 genomes]
rs4693743	0.89[CHB][hapmap];0.95[CHD][hapmap]
rs66596399	0.92[ASN][1000 genomes]
rs67631333	0.92[ASN][1000 genomes]
rs67886916	0.82[ASN][1000 genomes]
rs72658238	0.92[ASN][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	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	nsv879517	chr4:86677107-86739805	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86718200-86733800	Weak transcription	Gastric	stomach
2	chr4:86719400-86730800	Weak transcription	Primary B cells from cord blood	blood
3	chr4:86722000-86731400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr4:86727000-86729200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr4:86727000-86729200	Enhancers	Fetal Stomach	stomach
6	chr4:86727000-86730400	Enhancers	NHDF-Ad	bronchial
7	chr4:86727400-86730200	Enhancers	HSMM	muscle
8	chr4:86727400-86730800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:86727600-86729800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:86727600-86729800	Enhancers	HUVEC	blood vessel
11	chr4:86727800-86735800	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:86728000-86731000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr4:86728200-86747200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:86728400-86729800	Enhancers	Fetal Kidney	kidney
15	chr4:86728400-86730000	Enhancers	Fetal Heart	heart
16	chr4:86728600-86729200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr4:86728600-86729200	Enhancers	HMEC	breast
18	chr4:86728600-86729400	Flanking Active TSS	Osteobl	bone
19	chr4:86728600-86729600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:86728600-86729600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:86728600-86729600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:86728600-86729800	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr4:86728600-86729800	Enhancers	HSMMtube	muscle
24	chr4:86728600-86730000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:86728600-86730200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr4:86728600-86730400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr4:86728600-86730400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr4:86728600-86730800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr4:86728600-86731000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr4:86728800-86729200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr4:86728800-86729200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:86728800-86729200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr4:86728800-86729200	Enhancers	Right Ventricle	heart
34	chr4:86728800-86729400	Enhancers	Colon Smooth Muscle	Colon
35	chr4:86728800-86729600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr4:86728800-86729600	Enhancers	Brain Germinal Matrix	brain
37	chr4:86728800-86729800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:86728800-86729800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:86728800-86730000	Enhancers	H9 Cell Line	embryonic stem cell
40	chr4:86728800-86730000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:86728800-86730200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:86728800-86731000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr4:86729000-86729200	Enhancers	Adipose Nuclei	Adipose
44	chr4:86729000-86729200	Enhancers	NH-A	brain
45	chr4:86729000-86729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:86729000-86729600	Weak transcription	Pancreas	Pancrea
47	chr4:86729000-86729600	Weak transcription	Right Atrium	heart
48	chr4:86729000-86734000	Weak transcription	Left Ventricle	heart
49	chr4:86729000-86735600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr4:86729000-86739400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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