Variant report

Variant	rs12430760
Chromosome Location	chr13:52240365-52240366
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52238827..52243045-chr13:52243097..52246375,4	MCF-7	breast:
2	chr13:52236778..52240466-chr13:52241446..52244074,4	MCF-7	breast:
3	chr13:52025593..52028146-chr13:52239538..52242339,3	MCF-7	breast:
4	chr13:52025535..52027804-chr13:52238290..52241927,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1058141	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs10676	0.84[AMR][1000 genomes]
rs12427805	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs12428478	0.85[CEU][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes]
rs12430506	0.86[EUR][1000 genomes]
rs12430600	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs12431173	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17069413	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17075849	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17531181	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2011276	0.88[AMR][1000 genomes]
rs2296027	0.85[CEU][hapmap];0.84[AMR][1000 genomes]
rs2408491	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs55910561	0.88[AMR][1000 genomes]
rs57837262	0.88[AMR][1000 genomes]
rs59291282	0.89[AMR][1000 genomes]
rs73199739	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs73199742	0.96[AMR][1000 genomes]
rs73199750	0.88[AMR][1000 genomes]
rs7321346	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7329391	0.83[AMR][1000 genomes]
rs74086223	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8001480	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9568662	0.83[AMR][1000 genomes]
rs9596530	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs9596572	0.85[CEU][hapmap];0.86[AMR][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	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52219600-52253800	Weak transcription	Psoas Muscle	Psoas
2	chr13:52220400-52259000	Weak transcription	Thymus	Thymus
3	chr13:52221200-52253800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:52228400-52247000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr13:52228600-52248000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:52228600-52254000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:52229000-52248400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:52231600-52242800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr13:52231600-52249600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr13:52231800-52242400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr13:52231800-52244000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:52232200-52261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:52232800-52256400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr13:52233800-52240400	Weak transcription	Right Ventricle	heart
15	chr13:52234000-52277800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr13:52234200-52244600	Weak transcription	GM12878-XiMat	blood
17	chr13:52234200-52258800	Weak transcription	Adipose Nuclei	Adipose
18	chr13:52234200-52263200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr13:52234800-52257600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr13:52235200-52253800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:52235600-52240400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:52236600-52248600	Weak transcription	Lung	lung
23	chr13:52237000-52240600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr13:52237200-52240400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr13:52237200-52244600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:52237200-52257400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr13:52237200-52261400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr13:52237400-52240600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr13:52237400-52241600	Enhancers	Osteobl	bone
30	chr13:52237400-52244200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr13:52237400-52254400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr13:52237600-52240800	Enhancers	Brain Substantia Nigra	brain
33	chr13:52237600-52241800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:52237600-52248200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr13:52237800-52241200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:52238200-52240800	Enhancers	NHLF	lung
37	chr13:52238200-52241200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr13:52238200-52241400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr13:52238200-52241400	Enhancers	Brain Angular Gyrus	brain
40	chr13:52238200-52241600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:52238400-52242800	Enhancers	Liver	Liver
42	chr13:52238400-52250000	Weak transcription	Primary T cells from cord blood	blood
43	chr13:52238600-52240800	Strong transcription	Primary B cells from cord blood	blood
44	chr13:52238600-52244400	Weak transcription	Ovary	ovary
45	chr13:52238600-52247400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr13:52238600-52248400	Weak transcription	Left Ventricle	heart
47	chr13:52238600-52249600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr13:52238600-52256800	Weak transcription	Fetal Muscle Leg	muscle
49	chr13:52238600-52259400	Weak transcription	Fetal Stomach	stomach
50	chr13:52238800-52240400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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