Variant report

Variant	rs9858069
Chromosome Location	chr3:133945114-133945115
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	chr3:133944783..133948371-chr3:133966859..133970874,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163785	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10935104	0.90[CEU][hapmap]
rs1131262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707763	0.88[ASN][1000 genomes]
rs11915143	0.88[ASN][1000 genomes]
rs35322473	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3890774	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4072180	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4324466	0.89[ASN][1000 genomes]
rs4682664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682669	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55689708	0.81[ASN][1000 genomes]
rs56073423	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439465	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439466	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6650893	0.88[ASN][1000 genomes]
rs6762690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6776502	0.89[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6780295	0.88[ASN][1000 genomes]
rs6800143	0.89[ASN][1000 genomes]
rs6808085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355922	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7609611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9283588	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9812461	0.85[ASN][1000 genomes]
rs9818714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823873	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9825808	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827728	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9832732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9856298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9856792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9858707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
2	chr3:133894800-133946800	Weak transcription	Pancreas	Pancrea
3	chr3:133895000-133950000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:133895000-133950200	Weak transcription	Gastric	stomach
5	chr3:133919000-133950600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:133920800-133950200	Weak transcription	Aorta	Aorta
7	chr3:133920800-133950200	Weak transcription	Spleen	Spleen
8	chr3:133920800-133950600	Weak transcription	Hela-S3	cervix
9	chr3:133928600-133949400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:133930000-133950000	Weak transcription	NHDF-Ad	bronchial
11	chr3:133930000-133950400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:133930000-133954600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:133930200-133946400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:133930200-133950000	Weak transcription	HSMM	muscle
15	chr3:133930200-133950200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:133930200-133950600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:133930200-133955000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:133930200-133968000	Weak transcription	Fetal Kidney	kidney
19	chr3:133930400-133950200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:133930600-133957800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:133931400-133950200	Weak transcription	Dnd41	blood
22	chr3:133932400-133947000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:133932400-133951000	Weak transcription	NHLF	lung
24	chr3:133933600-133950000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:133934600-133950400	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:133935400-133954600	Weak transcription	HUVEC	blood vessel
27	chr3:133937600-133946800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:133938400-133950000	Weak transcription	Primary T cells from cord blood	blood
29	chr3:133938400-133950000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:133938600-133946800	Weak transcription	Osteobl	bone
31	chr3:133938800-133945600	Weak transcription	Primary B cells from cord blood	blood
32	chr3:133938800-133955200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:133939000-133949800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:133939000-133950000	Weak transcription	HSMMtube	muscle
35	chr3:133941000-133950200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:133941000-133954600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:133941000-133954800	Weak transcription	Fetal Intestine Large	intestine
38	chr3:133941000-133961600	Weak transcription	Esophagus	oesophagus
39	chr3:133941200-133950200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:133941200-133950200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:133941200-133950400	Weak transcription	Placenta	Placenta
42	chr3:133941400-133946800	Weak transcription	Fetal Intestine Small	intestine
43	chr3:133941400-133947400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:133941400-133950000	Weak transcription	Thymus	Thymus
45	chr3:133941400-133950800	Weak transcription	HepG2	liver
46	chr3:133941400-133957200	Weak transcription	Fetal Stomach	stomach
47	chr3:133941400-133967400	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:133942000-133951000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:133942000-133952600	Weak transcription	Brain Angular Gyrus	brain
50	chr3:133942200-133947000	Weak transcription	Rectal Smooth Muscle	rectum

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