Variant report

Variant	rs336292
Chromosome Location	chr4:143013388-143013389
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143006661..143009015-chr4:143011228..143013827,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10014809	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1039936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461275	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10461276	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12501744	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12509457	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13327961	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs168061	0.81[CHB][hapmap]
rs17015503	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2292392	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2322307	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2322308	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28413617	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28454477	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28460053	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28570218	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336295	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs336296	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336297	0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs336298	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336300	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs336308	0.86[CHB][hapmap]
rs336310	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs336312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336318	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336319	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs336321	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336323	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336324	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336331	0.81[ASN][1000 genomes]
rs336332	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs34087587	0.80[ASN][1000 genomes]
rs35981130	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3729592	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3756111	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3756112	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3756113	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3775621	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3775624	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3775625	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3775627	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3775628	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3775631	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3822135	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3822136	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3822137	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3822138	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3822139	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4388159	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4637485	0.80[ASN][1000 genomes]
rs4989471	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6537099	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6537100	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6537101	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6826672	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6827563	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6853327	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6853350	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9996933	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142948400-143029200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:142966000-143013800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:142988000-143015400	Weak transcription	Aorta	Aorta
4	chr4:142988200-143029400	Weak transcription	Left Ventricle	heart
5	chr4:142990000-143051200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:142997600-143014000	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:142997800-143024600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:143001400-143040600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:143002600-143041800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:143004000-143015400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:143004000-143017000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:143004000-143021800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:143004600-143051600	Weak transcription	Pancreas	Pancrea
14	chr4:143006200-143016400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:143007200-143014000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:143007200-143015400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:143007200-143016800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:143007400-143025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:143007600-143014000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:143007600-143024800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:143007800-143013800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:143007800-143015400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:143008000-143025600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:143008400-143014400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:143008600-143014000	Weak transcription	Dnd41	blood
26	chr4:143009200-143014000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:143009600-143013400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:143010000-143014600	Enhancers	NH-A	brain
29	chr4:143010400-143013400	Enhancers	NHEK	skin
30	chr4:143010400-143043400	Weak transcription	Psoas Muscle	Psoas
31	chr4:143010400-143057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:143011000-143015400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:143011600-143013400	Enhancers	HMEC	breast
34	chr4:143011600-143014000	Enhancers	HUVEC	blood vessel
35	chr4:143011600-143014400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:143012000-143013600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:143012400-143023000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr4:143012400-143040600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:143012600-143013400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr4:143012800-143013400	Enhancers	Fetal Heart	heart
41	chr4:143012800-143014200	Strong transcription	Primary T cells from cord blood	blood
42	chr4:143012800-143017400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:143013000-143013400	Enhancers	NHDF-Ad	bronchial
44	chr4:143013000-143014000	Weak transcription	HSMM	muscle
45	chr4:143013000-143014200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:143013000-143014200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:143013000-143016400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:143013000-143016400	Weak transcription	Osteobl	bone
49	chr4:143013000-143016600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:143013000-143016800	Weak transcription	Colon Smooth Muscle	Colon

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