Variant report

Variant	rs17490346
Chromosome Location	chr3:111570525-111570526
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	chr3:111568994..111570957-chr3:111577766..111580247,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1021706	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10934112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934114	1.00[JPT][hapmap]
rs10934116	0.93[EUR][1000 genomes]
rs1282970	1.00[JPT][hapmap]
rs1282975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1282977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1282978	0.96[EUR][1000 genomes]
rs1282980	0.96[EUR][1000 genomes]
rs1282981	0.96[EUR][1000 genomes]
rs1282984	0.96[EUR][1000 genomes]
rs1282992	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13063198	0.98[EUR][1000 genomes]
rs1913495	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3925080	1.00[JPT][hapmap]
rs3925081	1.00[JPT][hapmap]
rs3925082	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4381907	1.00[JPT][hapmap]
rs4383483	1.00[JPT][hapmap]
rs4682318	0.91[EUR][1000 genomes]
rs60787620	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637689	1.00[JPT][hapmap]
rs937553	1.00[JPT][hapmap]
rs937554	1.00[JPT][hapmap]
rs9841149	1.00[JPT][hapmap]
rs9842341	1.00[JPT][hapmap]
rs9847568	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9851613	0.93[JPT][hapmap]
rs9854765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9865074	1.00[JPT][hapmap]
rs9869555	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9872438	1.00[JPT][hapmap]

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	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111541200-111577600	Weak transcription	Pancreas	Pancrea
2	chr3:111563000-111577400	Weak transcription	HepG2	liver
3	chr3:111563800-111571200	Weak transcription	Stomach Mucosa	stomach
4	chr3:111565000-111571200	Enhancers	Placenta	Placenta
5	chr3:111565800-111570600	Weak transcription	HSMM	muscle
6	chr3:111566000-111571400	Weak transcription	Fetal Heart	heart
7	chr3:111566200-111577400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:111567200-111570800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:111567800-111577400	Weak transcription	Liver	Liver
10	chr3:111567800-111577400	Weak transcription	NHDF-Ad	bronchial
11	chr3:111568000-111571400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:111568400-111570600	Weak transcription	Fetal Intestine Large	intestine
13	chr3:111569400-111571800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:111569600-111571000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:111569600-111572200	Enhancers	Osteobl	bone
16	chr3:111570000-111571000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr3:111570000-111571200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:111570000-111571200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:111570000-111571600	Enhancers	HMEC	breast
20	chr3:111570000-111571600	Enhancers	NHLF	lung
21	chr3:111570000-111572000	Enhancers	NHEK	skin
22	chr3:111570000-111572200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:111570000-111572400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:111570200-111570600	Enhancers	Small Intestine	intestine
25	chr3:111570200-111570600	Flanking Active TSS	NH-A	brain
26	chr3:111570200-111570800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:111570200-111570800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:111570200-111570800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:111570200-111570800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:111570200-111570800	Enhancers	Fetal Stomach	stomach
31	chr3:111570200-111570800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr3:111570200-111571000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:111570200-111571000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr3:111570200-111571000	Flanking Active TSS	HUVEC	blood vessel
35	chr3:111570200-111571200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:111570200-111571200	Enhancers	A549	lung
37	chr3:111570200-111571600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr3:111570200-111571800	Enhancers	Adipose Nuclei	Adipose
39	chr3:111570200-111572400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:111570200-111572600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:111570200-111574400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:111570400-111570800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:111570400-111570800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:111570400-111570800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:111570400-111570800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:111570400-111570800	Enhancers	Thymus	Thymus
47	chr3:111570400-111570800	Enhancers	Hela-S3	cervix
48	chr3:111570400-111571000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:111570400-111571000	Enhancers	Fetal Kidney	kidney
50	chr3:111570400-111571200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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