Variant report

Variant	rs12494541
Chromosome Location	chr3:69218696-69218697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69217637..69219786-chr3:69225918..69228338,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12637416	0.84[ASN][1000 genomes]
rs4282065	0.99[ASN][1000 genomes]
rs4358306	0.88[ASN][1000 genomes]
rs4359814	0.89[ASN][1000 genomes]
rs4464459	0.96[ASN][1000 genomes]
rs4473559	0.97[ASN][1000 genomes]
rs67268350	0.86[ASN][1000 genomes]
rs6763046	0.91[ASN][1000 genomes]
rs6765197	0.92[ASN][1000 genomes]
rs6765309	0.84[ASN][1000 genomes]
rs7609655	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9310138	0.87[ASN][1000 genomes]
rs9310139	0.99[ASN][1000 genomes]
rs9310140	0.96[ASN][1000 genomes]
rs9853318	0.90[ASN][1000 genomes]
rs9872199	0.80[ASN][1000 genomes]
rs9872489	0.98[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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69209600-69228000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:69211200-69218800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:69211200-69219600	Weak transcription	Fetal Lung	lung
4	chr3:69211200-69219800	Weak transcription	Fetal Brain Female	brain
5	chr3:69211200-69219800	Weak transcription	Dnd41	blood
6	chr3:69211200-69226600	Weak transcription	Fetal Kidney	kidney
7	chr3:69211200-69229400	Weak transcription	Fetal Brain Male	brain
8	chr3:69211600-69220200	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:69211600-69220200	Weak transcription	Brain Substantia Nigra	brain
10	chr3:69211600-69223400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:69211600-69230200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:69211600-69231000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:69212200-69219800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:69213400-69225400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:69214200-69219800	Weak transcription	Placenta	Placenta
16	chr3:69214200-69226600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:69214800-69230400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:69215000-69220200	Weak transcription	Brain Anterior Caudate	brain
19	chr3:69215000-69220200	Weak transcription	Fetal Intestine Large	intestine
20	chr3:69215200-69220000	Weak transcription	Brain Germinal Matrix	brain
21	chr3:69215200-69220200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:69215200-69225400	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:69215600-69219400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:69215600-69225200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:69215800-69220600	Weak transcription	Right Ventricle	heart
26	chr3:69216000-69220000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:69216000-69220000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:69216000-69220400	Weak transcription	HMEC	breast
29	chr3:69216000-69225400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:69216000-69227200	Weak transcription	Pancreas	Pancrea
31	chr3:69216200-69220600	Weak transcription	Aorta	Aorta
32	chr3:69216200-69221000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:69216200-69229800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:69217000-69219800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:69217000-69219800	Weak transcription	HSMM	muscle
36	chr3:69217000-69220400	Weak transcription	Thymus	Thymus
37	chr3:69217200-69220200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:69217200-69225400	Weak transcription	Esophagus	oesophagus
39	chr3:69217200-69225400	Weak transcription	Fetal Stomach	stomach
40	chr3:69217200-69230200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:69217400-69219600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:69217400-69219800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:69217400-69220000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:69217400-69220200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:69217400-69220200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:69217400-69220400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:69217400-69229800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:69217600-69227400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:69217600-69230600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:69217800-69219400	Weak transcription	Monocytes-CD14+_RO01746	blood

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