Variant report

Variant	rs17425250
Chromosome Location	chr3:111593889-111593890
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	chr3:111589933..111591550-chr3:111593680..111595184,2	MCF-7	breast:
2	chr3:111581231..111584187-chr3:111592422..111594692,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17424938	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17490701	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17491175	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55921603	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55954252	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56092121	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56105878	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56343172	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67396907	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6809779	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73226343	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73226349	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73226359	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73226368	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73226399	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73228506	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73228508	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228510	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228514	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228515	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228518	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228521	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228530	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228535	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73228543	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73228545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228547	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228550	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228569	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228590	1.00[AFR][1000 genomes]
rs7340610	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs937557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][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	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
2	nsv980070	chr3:111592547-111602240	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111584600-111603400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:111585200-111622000	Weak transcription	HSMMtube	muscle
3	chr3:111585400-111603400	Weak transcription	Spleen	Spleen
4	chr3:111585400-111609000	Weak transcription	Esophagus	oesophagus
5	chr3:111587200-111597200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:111587200-111603000	Weak transcription	Placenta	Placenta
7	chr3:111587800-111599200	Weak transcription	Liver	Liver
8	chr3:111589200-111598400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:111589200-111603400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:111589800-111603400	Weak transcription	Pancreas	Pancrea
11	chr3:111591400-111594000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:111591400-111598400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:111591600-111598400	Weak transcription	Right Atrium	heart
14	chr3:111591600-111603200	Weak transcription	Ovary	ovary
15	chr3:111591600-111603600	Weak transcription	HepG2	liver
16	chr3:111591600-111610600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:111591600-111633200	Weak transcription	Fetal Kidney	kidney
18	chr3:111591800-111594000	Enhancers	Osteobl	bone
19	chr3:111592400-111594000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:111592400-111594000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr3:111592400-111594200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:111593000-111594400	Enhancers	HMEC	breast
23	chr3:111593400-111599600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:111593400-111601400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:111593600-111594200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:111593600-111594400	Weak transcription	Right Ventricle	heart
27	chr3:111593600-111598200	Weak transcription	Adipose Nuclei	Adipose
28	chr3:111593600-111598800	Weak transcription	Aorta	Aorta
29	chr3:111593600-111599000	Weak transcription	Left Ventricle	heart
30	chr3:111593600-111599200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:111593600-111601400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:111593600-111603000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:111593600-111603000	Weak transcription	Lung	lung
34	chr3:111593600-111603200	Weak transcription	Gastric	stomach
35	chr3:111593600-111603400	Weak transcription	HSMM	muscle
36	chr3:111593600-111608800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:111593800-111594400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:111593800-111594600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:111593800-111594600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:111593800-111595200	Genic enhancers	NHEK	skin
41	chr3:111593800-111596200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:111593800-111598800	Weak transcription	Hela-S3	cervix
43	chr3:111593800-111599000	Weak transcription	A549	lung
44	chr3:111593800-111599000	Weak transcription	NH-A	brain
45	chr3:111593800-111599200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:111593800-111601200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:111593800-111602000	Weak transcription	HUVEC	blood vessel
48	chr3:111593800-111602800	Weak transcription	NHLF	lung
49	chr3:111593800-111603000	Weak transcription	Fetal Stomach	stomach
50	chr3:111593800-111603200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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