Variant report

Variant	rs336378
Chromosome Location	chr4:143001573-143001574
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	chr4:142993302..142997726-chr4:142999331..143002418,4	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11729372	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11932936	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353603	1.00[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];1.00[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355425	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355426	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390990	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397735	1.00[CHB][hapmap]
rs1397738	0.82[AFR][1000 genomes]
rs1511252	0.81[CHD][hapmap]
rs1511253	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511255	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1849061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874575	1.00[MEX][hapmap]
rs189211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645786	1.00[MEX][hapmap]
rs2645788	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645796	1.00[MEX][hapmap]
rs2645799	0.81[CHD][hapmap]
rs2645800	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645810	0.81[CHD][hapmap]
rs2667094	0.86[JPT][hapmap]
rs2667095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667100	0.81[CHD][hapmap]
rs2667105	0.81[CHD][hapmap]
rs2667108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667109	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667117	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336293	0.85[ASN][1000 genomes]
rs336294	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs336299	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs336301	0.85[ASN][1000 genomes]
rs336302	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs336303	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs336304	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs336306	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs336309	1.00[MEX][hapmap]
rs336311	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs336313	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs336314	0.85[ASN][1000 genomes]
rs336316	0.85[ASN][1000 genomes]
rs336317	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs336320	1.00[MEX][hapmap]
rs336325	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs336327	0.85[ASN][1000 genomes]
rs336329	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336330	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap]
rs336336	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs336366	0.81[AFR][1000 genomes]
rs336368	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336370	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336372	1.00[ASN][1000 genomes]
rs336373	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336374	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs336379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336381	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775636	0.85[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs3775638	0.83[ASN][1000 genomes]
rs4342262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[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:41 , 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	chr4:142962200-143002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:142963400-143002200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:142966000-143010000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:142966000-143013800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:142978000-143002200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:142978200-143006200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:142985800-143011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:142988000-143015400	Weak transcription	Aorta	Aorta
11	chr4:142988200-143029400	Weak transcription	Left Ventricle	heart
12	chr4:142988400-143008600	Weak transcription	NHDF-Ad	bronchial
13	chr4:142990000-143051200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:142996800-143012600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:142997000-143006000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:142997600-143002000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:142997600-143014000	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:142997800-143001800	Weak transcription	HSMM	muscle
19	chr4:142997800-143002000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:142997800-143024600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:142998200-143001800	Weak transcription	HMEC	breast
22	chr4:142999800-143002200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:143000000-143001800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:143000200-143005000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:143000200-143006400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:143000400-143003800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:143000800-143002800	Enhancers	Fetal Heart	heart
28	chr4:143000800-143004200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:143001000-143003600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:143001000-143004600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:143001000-143004800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:143001200-143001600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:143001200-143001600	Enhancers	NHEK	skin
34	chr4:143001200-143003400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:143001200-143003800	Strong transcription	HSMMtube	muscle
36	chr4:143001200-143004000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr4:143001200-143004000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:143001200-143004400	Strong transcription	Primary T cells from cord blood	blood
39	chr4:143001400-143003600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:143001400-143003800	Strong transcription	Dnd41	blood
41	chr4:143001400-143040600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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