Variant report

Variant	rs2667090
Chromosome Location	chr4:142961991-142961992
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	chr4:142961970..142965946-chr4:142968550..142971585,4	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10018891	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519621	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs173060	0.90[EUR][1000 genomes]
rs1845971	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1912713	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1912714	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1912715	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1988510	1.00[EUR][1000 genomes]
rs1988511	1.00[EUR][1000 genomes]
rs2645809	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645825	1.00[EUR][1000 genomes]
rs2645827	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645828	1.00[EUR][1000 genomes]
rs2667082	1.00[EUR][1000 genomes]
rs2667087	1.00[CEU][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667088	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667089	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667091	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667120	1.00[EUR][1000 genomes]
rs336337	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336338	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336339	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336340	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336341	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336343	1.00[EUR][1000 genomes]
rs336344	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs336345	0.82[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336347	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336348	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336351	1.00[EUR][1000 genomes]
rs336352	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336354	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs336355	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs336356	1.00[CEU][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336357	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336358	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336359	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336360	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336362	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs336363	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs337232	0.90[EUR][1000 genomes]
rs6848572	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830096	chr4:142867099-143023761	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv428775	chr4:142943213-143050195	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv830097	chr4:142949705-143136372	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142943800-142965400	Weak transcription	Aorta	Aorta
2	chr4:142944200-142962800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:142945400-142983200	Weak transcription	Left Ventricle	heart
4	chr4:142947800-142977200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:142948400-143029200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:142949400-142977000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:142949600-142977000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:142950000-142962200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:142950200-142976600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:142954600-142968400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr4:142956600-142977000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:142956600-142977000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:142957000-142963000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:142957400-142976800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:142958200-142963200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:142958200-142975400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:142958400-142965000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:142958600-142964000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:142958600-142964000	Weak transcription	HSMM	muscle
20	chr4:142958800-142964000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr4:142958800-142964200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:142958800-142964600	Weak transcription	NHDF-Ad	bronchial
23	chr4:142958800-142964800	Weak transcription	HSMMtube	muscle
24	chr4:142959000-142968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:142959000-142977000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:142959000-142978000	Weak transcription	NHEK	skin
27	chr4:142959200-142995600	Weak transcription	Fetal Heart	heart
28	chr4:142960200-142967400	Weak transcription	Primary T cells from cord blood	blood
29	chr4:142960200-142973800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:142960600-142964400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr4:142961200-142962000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:142961200-142962200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:142961400-142963000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:142961600-142962800	Weak transcription	HUVEC	blood vessel
35	chr4:142961600-142976400	Weak transcription	Dnd41	blood
36	chr4:142961800-142964800	Weak transcription	HMEC	breast
37	chr4:142961800-143009600	Weak transcription	A549	lung

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