Variant report

Variant	rs336325
Chromosome Location	chr4:143007197-143007198
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	chr4:143006661..143009015-chr4:143011228..143013827,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11729372	0.83[ASN][1000 genomes]
rs11932936	0.85[ASN][1000 genomes]
rs1353603	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs1355425	0.85[ASN][1000 genomes]
rs1355426	0.85[ASN][1000 genomes]
rs1390987	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs1390988	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs1390990	0.85[ASN][1000 genomes]
rs1390991	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs1397735	0.82[CHB][hapmap]
rs1511252	0.81[CHD][hapmap]
rs1511253	0.85[ASN][1000 genomes]
rs1511255	0.85[ASN][1000 genomes]
rs1849061	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1874575	1.00[MEX][hapmap]
rs189211	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs1912712	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2130687	1.00[CEU][hapmap]
rs2645786	1.00[MEX][hapmap]
rs2645788	0.85[ASN][1000 genomes]
rs2645796	1.00[MEX][hapmap]
rs2645799	0.81[CHD][hapmap]
rs2645800	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2645810	0.81[CHD][hapmap]
rs2667095	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2667100	0.81[CHD][hapmap]
rs2667105	0.81[CHD][hapmap]
rs2667108	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs2667109	0.85[ASN][1000 genomes]
rs2667110	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2667117	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs2667118	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs336293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336301	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs336303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs336304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs336306	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs336309	1.00[MEX][hapmap]
rs336311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336313	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336314	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336316	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336317	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336320	1.00[MEX][hapmap]
rs336327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs336329	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs336330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs336336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[ASN][1000 genomes]
rs336368	0.85[ASN][1000 genomes]
rs336370	0.85[ASN][1000 genomes]
rs336372	0.85[ASN][1000 genomes]
rs336373	0.85[ASN][1000 genomes]
rs336374	0.85[ASN][1000 genomes]
rs336375	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs336376	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs336377	0.85[CHB][hapmap]
rs336378	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs336379	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs336380	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs336381	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs336382	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs336383	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs3775636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775638	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3775662	0.83[GIH][hapmap]
rs4342262	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs4499771	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs7695279	0.85[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142948400-143029200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:142961800-143009600	Weak transcription	A549	lung
3	chr4:142966000-143010000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:142966000-143013800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:142985800-143011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:142988000-143015400	Weak transcription	Aorta	Aorta
7	chr4:142988200-143029400	Weak transcription	Left Ventricle	heart
8	chr4:142988400-143008600	Weak transcription	NHDF-Ad	bronchial
9	chr4:142990000-143051200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:142996800-143012600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:142997600-143014000	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:142997800-143024600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:143001400-143040600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:143001600-143007800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:143001600-143010400	Weak transcription	NHEK	skin
16	chr4:143002000-143009000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:143002000-143011200	Weak transcription	HSMM	muscle
18	chr4:143002600-143010000	Weak transcription	Osteobl	bone
19	chr4:143002600-143041800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:143002800-143008000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:143002800-143009600	Weak transcription	Fetal Heart	heart
22	chr4:143004000-143015400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr4:143004000-143017000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:143004000-143021800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:143004600-143051600	Weak transcription	Pancreas	Pancrea
26	chr4:143004800-143010000	Weak transcription	HMEC	breast
27	chr4:143005400-143008400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr4:143005800-143009200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:143006000-143007200	Strong transcription	Primary T cells from cord blood	blood
30	chr4:143006000-143007200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:143006000-143007200	Strong transcription	HSMMtube	muscle
32	chr4:143006000-143007600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:143006000-143008400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:143006000-143008600	Strong transcription	Dnd41	blood
35	chr4:143006200-143007600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:143006200-143007800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:143006200-143007800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:143006200-143008400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:143006200-143012200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:143006200-143016400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:143006400-143007200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:143006400-143007200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:143006400-143007200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:143007000-143007200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:143007000-143007400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:143007000-143011600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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