Variant report

Variant	rs336352
Chromosome Location	chr4:142954671-142954672
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:142946395..142950633-chr4:142951002..142956006,4	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	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519621	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs173060	0.90[EUR][1000 genomes]
rs1845971	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1912713	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1912714	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1912715	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1988510	1.00[EUR][1000 genomes]
rs1988511	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645809	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645825	1.00[EUR][1000 genomes]
rs2645827	1.00[CEU][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645828	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667082	1.00[EUR][1000 genomes]
rs2667087	1.00[CEU][hapmap];0.80[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667088	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667089	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667090	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667091	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667120	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336337	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336339	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336340	1.00[CEU][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.94[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];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336348	1.00[CEU][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336351	1.00[EUR][1000 genomes]
rs336354	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs336355	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs336356	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336357	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336358	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336359	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336360	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336362	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs336363	1.00[CEU][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337232	0.90[EUR][1000 genomes]
rs6848572	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142941800-142957800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr4:142943800-142965400	Weak transcription	Aorta	Aorta
3	chr4:142944200-142955600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:142944200-142958600	Weak transcription	Fetal Intestine Small	intestine
5	chr4:142944200-142962800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:142945400-142954800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:142945400-142983200	Weak transcription	Left Ventricle	heart
8	chr4:142945600-142955800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:142947400-142958000	Weak transcription	HSMMtube	muscle
10	chr4:142947800-142977200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:142948200-142959800	Weak transcription	Dnd41	blood
12	chr4:142948400-143029200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:142949200-142958600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:142949400-142977000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:142949600-142955800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:142949600-142957800	Weak transcription	NHEK	skin
17	chr4:142949600-142977000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:142950000-142956200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:142950000-142957800	Weak transcription	HSMM	muscle
20	chr4:142950000-142962200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:142950200-142955400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr4:142950200-142955400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:142950200-142956600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:142950200-142957800	Weak transcription	HMEC	breast
25	chr4:142950200-142976600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:142950800-142956200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:142951800-142955000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:142951800-142956600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:142953000-142955400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:142954000-142957200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:142954200-142955800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:142954400-142957600	Strong transcription	Primary T cells from cord blood	blood
33	chr4:142954400-142958000	Weak transcription	Fetal Heart	heart
34	chr4:142954600-142958000	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:142954600-142968400	Weak transcription	Primary T cells fromperipheralblood	blood

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