Variant report

Variant	rs12637416
Chromosome Location	chr3:69219808-69219809
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69212011..69214078-chr3:69219051..69220759,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11128118	0.84[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11712024	0.80[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs12172924	0.95[ASN][1000 genomes]
rs12494541	0.84[ASN][1000 genomes]
rs13059488	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs13059687	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs13082480	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs28529735	0.89[ASN][1000 genomes]
rs4282065	0.85[ASN][1000 genomes]
rs4358306	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4464459	0.92[CHD][hapmap];0.93[GIH][hapmap];0.82[ASN][1000 genomes]
rs4473559	0.92[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4493438	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4504171	0.82[GIH][hapmap]
rs4508787	0.81[AFR][1000 genomes]
rs4541413	0.83[ASW][hapmap];0.84[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap];0.84[ASN][1000 genomes]
rs4624565	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs67268350	0.90[ASN][1000 genomes]
rs6763046	0.89[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6765197	0.91[ASN][1000 genomes]
rs6765309	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6792358	0.82[GIH][hapmap]
rs6804718	0.86[ASN][1000 genomes]
rs7609655	0.85[ASN][1000 genomes]
rs9310139	0.85[ASN][1000 genomes]
rs9310140	0.82[ASN][1000 genomes]
rs9831516	0.81[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap]
rs9833167	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs9836305	0.81[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap]
rs9838728	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9847983	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs9853318	0.89[ASN][1000 genomes]
rs9853587	0.83[ASW][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs9853744	0.88[ASN][1000 genomes]
rs9860235	0.90[JPT][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs9872199	0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap]
rs9872489	0.82[ASN][1000 genomes]
rs9875511	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[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:79 , 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	chr3:69211600-69220200	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:69211600-69220200	Weak transcription	Brain Substantia Nigra	brain
6	chr3:69211600-69223400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:69211600-69230200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:69211600-69231000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:69213400-69225400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:69214200-69226600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:69214800-69230400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:69215000-69220200	Weak transcription	Brain Anterior Caudate	brain
13	chr3:69215000-69220200	Weak transcription	Fetal Intestine Large	intestine
14	chr3:69215200-69220000	Weak transcription	Brain Germinal Matrix	brain
15	chr3:69215200-69220200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:69215200-69225400	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:69215600-69225200	Weak transcription	Fetal Intestine Small	intestine
18	chr3:69215800-69220600	Weak transcription	Right Ventricle	heart
19	chr3:69216000-69220000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:69216000-69220000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:69216000-69220400	Weak transcription	HMEC	breast
22	chr3:69216000-69225400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:69216000-69227200	Weak transcription	Pancreas	Pancrea
24	chr3:69216200-69220600	Weak transcription	Aorta	Aorta
25	chr3:69216200-69221000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:69216200-69229800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:69217000-69220400	Weak transcription	Thymus	Thymus
28	chr3:69217200-69220200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:69217200-69225400	Weak transcription	Esophagus	oesophagus
30	chr3:69217200-69225400	Weak transcription	Fetal Stomach	stomach
31	chr3:69217200-69230200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:69217400-69220000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:69217400-69220200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:69217400-69220200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:69217400-69220400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:69217400-69229800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:69217600-69227400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:69217600-69230600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:69218000-69220400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:69218200-69220200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr3:69218200-69220800	Weak transcription	Fetal Heart	heart
42	chr3:69218200-69223000	Strong transcription	HUVEC	blood vessel
43	chr3:69218200-69223800	Strong transcription	Liver	Liver
44	chr3:69218400-69220200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:69218400-69220600	Weak transcription	Fetal Thymus	thymus
46	chr3:69218400-69230000	Weak transcription	Hela-S3	cervix
47	chr3:69218400-69247400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:69218400-69247800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:69218600-69220200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:69218600-69220200	Weak transcription	Left Ventricle	heart

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