Variant report

Variant	rs489398
Chromosome Location	chr3:135995498-135995499
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	chr3:135967984..135969714-chr3:135993096..135996031,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114054	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1145101	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13071085	1.00[ASN][1000 genomes]
rs17252498	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821445	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503973	0.83[AMR][1000 genomes]
rs610860	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789601	0.89[EUR][1000 genomes]
rs696517	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8045	0.82[AMR][1000 genomes]
rs866782	0.88[AMR][1000 genomes];0.95[EUR][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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970200-135996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:135970600-135998800	Weak transcription	Fetal Brain Male	brain
3	chr3:135970600-135999200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:135970600-135999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:135970800-135998000	Weak transcription	Hela-S3	cervix
7	chr3:135974800-135997800	Weak transcription	Stomach Mucosa	stomach
8	chr3:135976200-135996000	Weak transcription	Pancreas	Pancrea
9	chr3:135976200-135999400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:135976200-136012400	Weak transcription	NHLF	lung
11	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
12	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:135977400-135995600	Weak transcription	Fetal Lung	lung
14	chr3:135977400-135996000	Weak transcription	K562	blood
15	chr3:135980800-135995600	Weak transcription	Right Ventricle	heart
16	chr3:135980800-135997600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:135980800-135999200	Weak transcription	Small Intestine	intestine
18	chr3:135981000-135998600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:135981200-135999200	Weak transcription	NHDF-Ad	bronchial
20	chr3:135981200-136052000	Weak transcription	NH-A	brain
21	chr3:135981600-135997200	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:135981600-135998000	Weak transcription	Fetal Heart	heart
23	chr3:135981600-135998800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
25	chr3:135981800-135995600	Weak transcription	Gastric	stomach
26	chr3:135981800-135999600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:135982600-135997800	Weak transcription	HSMMtube	muscle
28	chr3:135982600-135999000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:135982600-136004000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:135982800-135995600	Weak transcription	Lung	lung
31	chr3:135982800-135995800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:135984000-135996400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:135984600-135995800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:135984600-135996600	Weak transcription	HSMM	muscle
35	chr3:135984600-135998000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:135984600-135998000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:135985600-135999400	Weak transcription	Osteobl	bone
38	chr3:135985800-135997600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:135986200-135995600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:135986400-135995600	Weak transcription	Esophagus	oesophagus
41	chr3:135986400-135995800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:135986400-135995800	Weak transcription	Aorta	Aorta
43	chr3:135986400-135998200	Weak transcription	A549	lung
44	chr3:135986800-135997600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:135987800-135998000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:135988000-135995600	Weak transcription	Fetal Thymus	thymus
47	chr3:135988000-135995600	Weak transcription	Ovary	ovary
48	chr3:135988000-135999200	Weak transcription	Thymus	Thymus
49	chr3:135988400-135995600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:135988400-135995600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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