Variant report

Variant	rs2645800
Chromosome Location	chr4:142970539-142970540
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: 66 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11729372	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11932936	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353603	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355425	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355426	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390987	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390988	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390990	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390991	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397735	1.00[CHB][hapmap]
rs1511253	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511255	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1849061	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189211	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912712	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645788	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667094	0.82[JPT][hapmap]
rs2667095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667108	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667109	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667110	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667117	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667118	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336293	0.85[ASN][1000 genomes]
rs336294	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs336299	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs336301	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs336302	0.83[ASN][1000 genomes]
rs336303	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs336304	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs336306	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs336311	0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs336313	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs336314	0.85[ASN][1000 genomes]
rs336316	0.85[ASN][1000 genomes]
rs336317	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs336325	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs336327	0.85[ASN][1000 genomes]
rs336329	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336330	0.82[JPT][hapmap]
rs336336	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs336368	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336370	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336372	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs336373	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336374	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336375	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336376	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336377	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs336378	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336379	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336380	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336381	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336382	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336383	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775636	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs3775638	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4342262	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499771	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695279	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142945400-142983200	Weak transcription	Left Ventricle	heart
2	chr4:142947800-142977200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:142948400-143029200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:142949400-142977000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:142949600-142977000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:142950200-142976600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:142956600-142977000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:142956600-142977000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:142957400-142976800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:142958200-142975400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr4:142959000-142977000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:142959000-142978000	Weak transcription	NHEK	skin
13	chr4:142959200-142995600	Weak transcription	Fetal Heart	heart
14	chr4:142960200-142973800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:142961600-142976400	Weak transcription	Dnd41	blood
16	chr4:142961800-143009600	Weak transcription	A549	lung
17	chr4:142962200-143002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:142963400-143001000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:142963400-143002200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:142965200-142983400	Weak transcription	HMEC	breast
21	chr4:142965800-142976800	Weak transcription	NHDF-Ad	bronchial
22	chr4:142965800-142977000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:142966000-142977000	Weak transcription	HSMMtube	muscle
24	chr4:142966000-142987000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:142966000-142987600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:142966000-143010000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:142966000-143013800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:142967200-142975600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:142968000-142977000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:142969000-142975600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr4:142969600-142976000	Weak transcription	HSMM	muscle
32	chr4:142970000-142973600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:142970200-142973800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:142970200-142974000	Weak transcription	Primary T cells from cord blood	blood
35	chr4:142970400-142974000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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