Variant report

Variant	rs336306
Chromosome Location	chr4:143019812-143019813
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143018754..143020846-chr4:143024197..143025698,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11729372	0.80[ASN][1000 genomes]
rs11932936	0.83[ASN][1000 genomes]
rs1353603	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs1355425	0.83[ASN][1000 genomes]
rs1355426	0.83[ASN][1000 genomes]
rs1390987	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs1390988	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs1390990	0.83[ASN][1000 genomes]
rs1390991	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs1397735	0.82[CHB][hapmap]
rs1511252	0.90[CHD][hapmap]
rs1511253	0.83[ASN][1000 genomes]
rs1511255	0.83[ASN][1000 genomes]
rs1849061	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1874575	1.00[MEX][hapmap]
rs189211	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs1912712	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2130687	1.00[CEU][hapmap]
rs2645786	1.00[MEX][hapmap]
rs2645788	0.83[ASN][1000 genomes]
rs2645796	1.00[MEX][hapmap]
rs2645799	0.90[CHD][hapmap]
rs2645800	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2645810	0.90[CHD][hapmap]
rs2667095	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2667100	0.90[CHD][hapmap]
rs2667105	0.90[CHD][hapmap]
rs2667108	0.85[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs2667109	0.83[ASN][1000 genomes]
rs2667110	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2667117	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs2667118	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs336293	0.97[ASN][1000 genomes]
rs336294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs336299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs336301	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs336302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][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]
rs336309	1.00[MEX][hapmap]
rs336311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs336313	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];0.91[MKK][hapmap];0.89[YRI][hapmap];0.97[ASN][1000 genomes]
rs336314	0.97[ASN][1000 genomes]
rs336316	0.97[ASN][1000 genomes]
rs336317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs336320	1.00[MEX][hapmap]
rs336325	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]
rs336327	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs336329	0.85[CHB][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs336330	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs336368	0.83[ASN][1000 genomes]
rs336370	0.83[ASN][1000 genomes]
rs336372	0.83[ASN][1000 genomes]
rs336373	0.83[ASN][1000 genomes]
rs336374	0.83[ASN][1000 genomes]
rs336375	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs336376	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs336377	0.85[CHB][hapmap]
rs336378	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs336379	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs336380	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs336381	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs336382	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs336383	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs3775636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3775638	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775662	0.83[GIH][hapmap]
rs4342262	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs4499771	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs7695279	0.85[CHB][hapmap];0.83[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs336306	C2CD4B	trans	brain	seeQTL
rs336306	CSF3	trans	brain	seeQTL

Chromatin state (count:49 , 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	chr4:142988200-143029400	Weak transcription	Left Ventricle	heart
3	chr4:142990000-143051200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:142997800-143024600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:143001400-143040600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:143002600-143041800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:143004000-143021800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:143004600-143051600	Weak transcription	Pancreas	Pancrea
9	chr4:143007400-143025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:143007600-143024800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:143008000-143025600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:143010400-143043400	Weak transcription	Psoas Muscle	Psoas
13	chr4:143010400-143057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:143012400-143023000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr4:143012400-143040600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:143014000-143035800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr4:143014200-143021800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:143014400-143022600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:143014600-143026200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:143014600-143049600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:143015800-143027400	Weak transcription	Aorta	Aorta
22	chr4:143015800-143049600	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:143016000-143024600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:143016400-143024400	Strong transcription	Primary T cells from cord blood	blood
25	chr4:143016600-143030800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:143017600-143025400	Weak transcription	Dnd41	blood
27	chr4:143017800-143044400	Weak transcription	Fetal Heart	heart
28	chr4:143018000-143031000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:143018200-143020000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:143018200-143020000	Weak transcription	Hela-S3	cervix
31	chr4:143018200-143020000	Weak transcription	NHDF-Ad	bronchial
32	chr4:143018200-143021000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:143018200-143021200	Weak transcription	HSMMtube	muscle
34	chr4:143018200-143021400	Weak transcription	HUVEC	blood vessel
35	chr4:143018200-143022000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr4:143018200-143022400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:143018200-143029000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:143018200-143033400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr4:143018800-143020000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:143018800-143029000	Weak transcription	NHEK	skin
41	chr4:143018800-143109600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr4:143019000-143020000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr4:143019200-143023000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:143019200-143024200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:143019600-143022600	Weak transcription	A549	lung
46	chr4:143019600-143023200	Strong transcription	HSMM	muscle
47	chr4:143019800-143020200	Strong transcription	HMEC	breast
48	chr4:143019800-143025800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:143019800-143026400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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