Variant report

Variant	rs1398747
Chromosome Location	chr3:111412273-111412274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111410859..111413288-chr3:111426130..111428349,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13078891	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13086157	0.85[CEU][hapmap]
rs1355767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1553970	0.82[CEU][hapmap]
rs1606503	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2036995	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2036996	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35957576	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4481128	0.81[EUR][1000 genomes]
rs4682052	0.85[CEU][hapmap]
rs4682295	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62275506	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs867293	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111395800-111413400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:111406200-111426800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:111407600-111412800	Weak transcription	Small Intestine	intestine
4	chr3:111409400-111412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:111409400-111412600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:111409400-111413400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:111409400-111414000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:111409400-111415600	Enhancers	Hela-S3	cervix
9	chr3:111409600-111412600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:111409600-111412600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:111409600-111413400	Weak transcription	Fetal Thymus	thymus
12	chr3:111409600-111415000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:111410000-111413000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:111410000-111413000	Weak transcription	NHDF-Ad	bronchial
15	chr3:111410200-111412400	Weak transcription	HSMMtube	muscle
16	chr3:111410200-111413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:111410200-111413600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:111410200-111414200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:111410200-111417200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:111410200-111426800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:111410200-111428400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:111410200-111433200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:111410400-111412600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:111410400-111413000	Weak transcription	NHEK	skin
25	chr3:111410400-111413200	Weak transcription	HMEC	breast
26	chr3:111410400-111413200	Weak transcription	Osteobl	bone
27	chr3:111410400-111413400	Weak transcription	HSMM	muscle
28	chr3:111410400-111413400	Weak transcription	NH-A	brain
29	chr3:111410400-111414200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:111410600-111413000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:111410600-111443400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:111410800-111418200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:111410800-111419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:111411600-111412400	Enhancers	Primary T cells from cord blood	blood
35	chr3:111411600-111412400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr3:111411600-111412600	Enhancers	Fetal Heart	heart
37	chr3:111411600-111412800	Enhancers	Duodenum Mucosa	Duodenum
38	chr3:111411600-111413200	Enhancers	GM12878-XiMat	blood
39	chr3:111411600-111413400	Enhancers	Primary B cells from peripheral blood	blood
40	chr3:111411600-111413600	Enhancers	Fetal Intestine Small	intestine
41	chr3:111411600-111413800	Enhancers	Fetal Intestine Large	intestine
42	chr3:111411600-111416200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:111411800-111412400	Enhancers	Primary B cells from cord blood	blood
44	chr3:111412000-111412400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:111412000-111412400	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:111412000-111412400	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr3:111412200-111412600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr3:111412200-111413200	Weak transcription	A549	lung
49	chr3:111412200-111414400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:111412200-111426800	Weak transcription	Rectal Mucosa Donor 29	rectum

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