Variant report

Variant	rs2399394
Chromosome Location	chr3:111439158-111439159
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	chr3:111436461..111439454-chr3:111578478..111580162,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1105448	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494734	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13061461	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13083322	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs13086018	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1398751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1398753	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1398754	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16858448	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2292518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821919	0.88[CEU][hapmap]
rs4401340	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4414820	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682298	0.86[JPT][hapmap]
rs7624162	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7646161	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7646453	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs882591	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs938219	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854875	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111410600-111443400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
3	chr3:111418200-111442000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:111420400-111450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:111420600-111445600	Weak transcription	HepG2	liver
6	chr3:111424600-111441800	Weak transcription	Thymus	Thymus
7	chr3:111425800-111441200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:111425800-111443800	Weak transcription	Dnd41	blood
9	chr3:111427000-111442400	Weak transcription	Ovary	ovary
10	chr3:111427200-111448400	Weak transcription	Right Ventricle	heart
11	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:111428800-111445200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:111429000-111441000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:111429400-111446800	Weak transcription	Fetal Intestine Large	intestine
16	chr3:111429600-111442400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:111431400-111441600	Weak transcription	Fetal Stomach	stomach
18	chr3:111431600-111439600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:111431600-111440000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:111431600-111443800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:111431600-111443800	Weak transcription	Fetal Brain Female	brain
22	chr3:111431600-111451400	Weak transcription	Gastric	stomach
23	chr3:111432000-111440400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:111432000-111442200	Weak transcription	HSMM	muscle
25	chr3:111432000-111448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:111432000-111448600	Weak transcription	Brain Germinal Matrix	brain
27	chr3:111432200-111442200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:111432400-111445000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:111433600-111439200	Weak transcription	Placenta	Placenta
30	chr3:111433600-111441600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:111433600-111444000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:111433800-111447000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:111434000-111442000	Weak transcription	HSMMtube	muscle
34	chr3:111434000-111443400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:111434200-111442600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:111435200-111439200	Weak transcription	Fetal Thymus	thymus
38	chr3:111435200-111439600	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:111435200-111447800	Weak transcription	HUVEC	blood vessel
40	chr3:111435600-111442200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:111436000-111439600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:111436400-111439600	Weak transcription	Left Ventricle	heart
43	chr3:111436800-111439800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:111436800-111440000	Weak transcription	Adipose Nuclei	Adipose
45	chr3:111436800-111441400	Weak transcription	Hela-S3	cervix
46	chr3:111436800-111442000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr3:111436800-111442000	Weak transcription	NH-A	brain
48	chr3:111436800-111442200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:111436800-111442200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:111436800-111442200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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