Variant report

Variant	rs4473559
Chromosome Location	chr3:69222863-69222864
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69221873..69224471-chr3:69354670..69357098,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11128118	0.92[GIH][hapmap];0.81[JPT][hapmap]
rs11712024	0.81[JPT][hapmap]
rs12172924	0.83[ASN][1000 genomes]
rs12494541	0.97[ASN][1000 genomes]
rs12637416	0.92[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs13059488	0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs13059687	0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs4282065	0.98[ASN][1000 genomes]
rs4358306	0.91[ASN][1000 genomes]
rs4359814	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4450819	0.83[ASN][1000 genomes]
rs4464459	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4508786	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4541413	1.00[GIH][hapmap]
rs4624565	0.83[ASN][1000 genomes]
rs57600863	1.00[EUR][1000 genomes]
rs58068554	1.00[EUR][1000 genomes]
rs67268350	0.89[ASN][1000 genomes]
rs6763046	0.80[ASW][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6765197	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6765309	0.83[ASN][1000 genomes]
rs72928330	1.00[EUR][1000 genomes]
rs72930208	1.00[EUR][1000 genomes]
rs7609655	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9310138	0.86[ASN][1000 genomes]
rs9310139	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9310140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9831516	0.81[ASW][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MKK][hapmap];0.82[ASN][1000 genomes]
rs9833167	0.83[ASN][1000 genomes]
rs9836305	0.81[ASW][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MKK][hapmap];0.82[ASN][1000 genomes]
rs9838728	0.81[ASN][1000 genomes]
rs9847983	0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs9853318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9860235	0.83[ASN][1000 genomes]
rs9872199	1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9872489	0.99[ASN][1000 genomes]
rs9875511	0.81[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:86 , 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	chr3:69211200-69226600	Weak transcription	Fetal Kidney	kidney
3	chr3:69211200-69229400	Weak transcription	Fetal Brain Male	brain
4	chr3:69211600-69223400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:69211600-69230200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:69211600-69231000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:69213400-69225400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:69214200-69226600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:69214800-69230400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:69215200-69225400	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:69215600-69225200	Weak transcription	Fetal Intestine Small	intestine
12	chr3:69216000-69225400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:69216000-69227200	Weak transcription	Pancreas	Pancrea
14	chr3:69216200-69229800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:69217200-69225400	Weak transcription	Esophagus	oesophagus
16	chr3:69217200-69225400	Weak transcription	Fetal Stomach	stomach
17	chr3:69217200-69230200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:69217400-69229800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:69217600-69227400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:69217600-69230600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:69218200-69223000	Strong transcription	HUVEC	blood vessel
22	chr3:69218200-69223800	Strong transcription	Liver	Liver
23	chr3:69218400-69230000	Weak transcription	Hela-S3	cervix
24	chr3:69218400-69247400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:69218400-69247800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:69218600-69224600	Weak transcription	HSMMtube	muscle
27	chr3:69218600-69228000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:69218600-69228200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:69218600-69228400	Weak transcription	Adipose Nuclei	Adipose
30	chr3:69218800-69227600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:69218800-69228400	Weak transcription	Colonic Mucosa	Colon
32	chr3:69219000-69227200	Weak transcription	Small Intestine	intestine
33	chr3:69219200-69230000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:69219400-69226000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:69219400-69227000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:69219600-69227000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:69219800-69223600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:69219800-69230800	Strong transcription	Placenta	Placenta
39	chr3:69220600-69229600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:69220800-69224200	Weak transcription	Brain Germinal Matrix	brain
41	chr3:69220800-69225400	Weak transcription	Spleen	Spleen
42	chr3:69220800-69229800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:69220800-69231600	Weak transcription	Psoas Muscle	Psoas
44	chr3:69221000-69223400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:69221000-69224000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:69221000-69224600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:69221000-69225000	Weak transcription	Fetal Thymus	thymus
48	chr3:69221000-69227000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:69221000-69227000	Weak transcription	Gastric	stomach
50	chr3:69221000-69227000	Weak transcription	Thymus	Thymus

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