Variant report

Variant	rs1989180
Chromosome Location	chr3:143549639-143549640
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	chr3:143548374..143549959-chr3:143555685..143558599,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10433437	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12497227	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1394403	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs16854417	0.90[CHB][hapmap]
rs16854421	0.90[CHB][hapmap]
rs16854423	0.90[CHB][hapmap]
rs16854424	0.90[CHB][hapmap]
rs16854463	0.90[CHB][hapmap]
rs16854493	0.90[CHB][hapmap]
rs16854503	1.00[CHB][hapmap]
rs16854525	0.90[CHB][hapmap]
rs1823220	0.90[CHB][hapmap]
rs1900643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134913	0.92[AMR][1000 genomes]
rs2361199	0.90[CHB][hapmap]
rs2361204	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4839613	0.82[CEU][hapmap]
rs4839614	0.90[CHB][hapmap]
rs4839659	0.90[CHB][hapmap]
rs4839660	0.90[CHB][hapmap]
rs4839661	0.90[CHB][hapmap]
rs4839663	0.90[CHB][hapmap]
rs4839670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763660	0.82[CHB][hapmap]
rs6764661	1.00[CHB][hapmap];0.92[AMR][1000 genomes]
rs6765414	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs6769847	0.90[CHB][hapmap]
rs6776336	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes]
rs6792031	0.90[CHB][hapmap]
rs6804065	0.90[CHB][hapmap]
rs7621206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7651412	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652644	0.90[CHB][hapmap]
rs9822158	0.90[CHB][hapmap]
rs9827103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9832471	1.00[CHB][hapmap];0.92[AMR][1000 genomes]
rs9847107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr3:143539600-143550000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:143539800-143558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:143541000-143554200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:143541400-143565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:143541800-143549800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:143542000-143553600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:143542200-143549800	Weak transcription	Brain Anterior Caudate	brain
8	chr3:143542200-143552400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:143542200-143553600	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:143543600-143551400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:143544000-143549800	Weak transcription	Adipose Nuclei	Adipose
12	chr3:143544200-143552800	Weak transcription	Fetal Lung	lung
13	chr3:143545000-143549800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:143545400-143549800	Weak transcription	Brain Substantia Nigra	brain
15	chr3:143545400-143550000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:143545400-143550000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:143545400-143550200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:143545400-143550400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:143545400-143550400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:143545400-143558800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:143545600-143565400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:143545800-143549800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:143545800-143550000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:143545800-143551000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:143546000-143550200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:143546000-143559000	Weak transcription	Primary B cells from cord blood	blood
27	chr3:143546200-143549800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:143546800-143550200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:143547000-143558200	Weak transcription	Esophagus	oesophagus
30	chr3:143548600-143549800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:143548800-143550000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:143548800-143551600	Enhancers	Stomach Mucosa	stomach
33	chr3:143548800-143551600	Enhancers	NHLF	lung
34	chr3:143548800-143551800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:143548800-143551800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:143549000-143549800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:143549000-143549800	Enhancers	GM12878-XiMat	blood
38	chr3:143549000-143550000	Enhancers	NHDF-Ad	bronchial
39	chr3:143549000-143550400	Enhancers	Primary hematopoietic stem cells	blood
40	chr3:143549000-143551000	Enhancers	HUVEC	blood vessel
41	chr3:143549000-143551800	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:143549000-143551800	Enhancers	HMEC	breast
43	chr3:143549000-143552800	Enhancers	Colon Smooth Muscle	Colon
44	chr3:143549200-143550000	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr3:143549200-143550000	Enhancers	NHEK	skin
46	chr3:143549200-143551000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr3:143549200-143565200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:143549400-143549800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:143549400-143550600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:143549400-143552400	Weak transcription	Aorta	Aorta

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