Variant report

Variant	rs17488681
Chromosome Location	chr3:111391464-111391465
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	chr3:111388505..111391497-chr3:111391977..111394861,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240891	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17281311	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17423232	0.94[CEU][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17488841	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73228199	0.86[AMR][1000 genomes]
rs73230104	0.86[AMR][1000 genomes]
rs73230106	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73230108	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73230114	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73230118	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73230122	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73230126	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73230140	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73230146	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73230153	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73230160	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73230162	0.80[EUR][1000 genomes]
rs73230168	0.94[AMR][1000 genomes];0.99[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	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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111385000-111392600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:111385400-111392600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:111386800-111392400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:111387000-111392400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:111387000-111392600	Enhancers	Primary T cells from cord blood	blood
6	chr3:111387000-111392600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:111387000-111392600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:111387800-111392600	Weak transcription	GM12878-XiMat	blood
9	chr3:111388000-111391600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:111388000-111392000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:111388000-111392200	Weak transcription	Thymus	Thymus
12	chr3:111388000-111392400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:111388200-111391800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:111388200-111391800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:111388200-111392200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:111388200-111392400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:111388200-111392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:111388400-111392200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:111388400-111392400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:111388400-111392400	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:111388400-111392600	Weak transcription	HUVEC	blood vessel
22	chr3:111388600-111392600	Weak transcription	Fetal Intestine Large	intestine
23	chr3:111388600-111392600	Weak transcription	Fetal Intestine Small	intestine
24	chr3:111388800-111392400	Weak transcription	Hela-S3	cervix
25	chr3:111388800-111392600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:111389200-111392400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:111389200-111392600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:111389200-111392600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:111389200-111392600	Weak transcription	NHDF-Ad	bronchial
30	chr3:111389200-111392600	Weak transcription	NHLF	lung
31	chr3:111389200-111392800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:111389200-111392800	Weak transcription	HSMMtube	muscle
33	chr3:111389200-111393000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:111389400-111392400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:111389400-111392400	Weak transcription	HMEC	breast
36	chr3:111389400-111392400	Weak transcription	NHEK	skin
37	chr3:111389400-111392600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:111389400-111392600	Weak transcription	A549	lung
39	chr3:111389400-111392800	Weak transcription	HSMM	muscle
40	chr3:111389600-111392200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:111389600-111392600	Weak transcription	NH-A	brain
42	chr3:111389600-111392800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:111389800-111392200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr3:111389800-111392400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:111389800-111392400	Weak transcription	Placenta	Placenta
46	chr3:111389800-111392600	Weak transcription	Osteobl	bone
47	chr3:111389800-111392800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:111390000-111392400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:111390000-111392400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:111390000-111392600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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