Variant report

Variant	rs3775648
Chromosome Location	chr4:143049620-143049621
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	chr4:143048538..143050644-chr4:143051888..143053940,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10000975	0.89[ASN][1000 genomes]
rs10003401	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10003713	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10006183	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10006255	0.89[ASN][1000 genomes]
rs10006284	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10006285	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10010617	0.82[CEU][hapmap]
rs10013826	0.82[CEU][hapmap]
rs10018171	0.88[ASN][1000 genomes]
rs10018345	0.89[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs10026164	0.82[CEU][hapmap]
rs10026333	0.88[ASN][1000 genomes]
rs10027089	0.82[CEU][hapmap]
rs10029467	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10030014	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10030954	0.87[ASN][1000 genomes]
rs10032149	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10032157	0.88[ASN][1000 genomes]
rs10032328	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10032526	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10033103	0.88[ASN][1000 genomes]
rs1039133	0.82[CEU][hapmap]
rs10519618	0.81[JPT][hapmap]
rs12330961	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12331260	0.93[ASN][1000 genomes]
rs12498546	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12500675	0.86[ASN][1000 genomes]
rs12500731	0.88[ASN][1000 genomes]
rs12501475	0.81[JPT][hapmap]
rs12502469	0.86[ASN][1000 genomes]
rs12503726	0.82[CEU][hapmap]
rs12505349	0.81[JPT][hapmap]
rs12508643	0.85[ASN][1000 genomes]
rs12511892	0.83[ASN][1000 genomes]
rs12639889	0.83[ASN][1000 genomes]
rs12639936	0.83[ASN][1000 genomes]
rs12640533	0.82[ASN][1000 genomes]
rs12640550	0.87[ASN][1000 genomes]
rs12641407	0.91[ASN][1000 genomes]
rs12642708	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12642756	0.89[ASN][1000 genomes]
rs12643489	0.82[CEU][hapmap]
rs17015544	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17015559	0.93[ASN][1000 genomes]
rs17015598	0.82[CEU][hapmap]
rs1907123	0.82[CEU][hapmap]
rs1907136	0.82[CEU][hapmap]
rs2055211	0.82[CEU][hapmap]
rs2270657	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2270658	0.90[ASN][1000 genomes]
rs2270659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2276942	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2627805	0.82[CEU][hapmap]
rs2627821	0.82[CEU][hapmap]
rs28373344	0.93[ASN][1000 genomes]
rs28458916	0.90[ASN][1000 genomes]
rs28588595	0.90[ASN][1000 genomes]
rs28605546	0.85[ASN][1000 genomes]
rs28708386	0.88[ASN][1000 genomes]
rs3756117	0.87[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs3775616	0.81[JPT][hapmap]
rs3775630	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3775639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3775640	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3775641	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3775642	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3775643	0.90[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs3775644	0.96[ASN][1000 genomes]
rs3775647	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775649	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775650	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775651	0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775652	0.81[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs3775653	0.81[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs3775654	0.81[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs3775655	0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs3775656	0.91[ASN][1000 genomes]
rs3775657	0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3775658	0.81[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs3775674	0.82[CEU][hapmap]
rs3822140	0.89[ASN][1000 genomes]
rs4956318	0.82[CEU][hapmap]
rs4956436	0.82[CEU][hapmap]
rs4956437	0.82[CEU][hapmap]
rs55666838	0.84[ASN][1000 genomes]
rs55679069	0.95[ASN][1000 genomes]
rs55728718	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55784399	0.96[ASN][1000 genomes]
rs56024852	0.96[ASN][1000 genomes]
rs56156331	0.96[ASN][1000 genomes]
rs56334109	0.84[ASN][1000 genomes]
rs58531376	0.89[ASN][1000 genomes]
rs67277330	0.88[ASN][1000 genomes]
rs6813782	0.89[ASN][1000 genomes]
rs6813798	0.86[ASN][1000 genomes]
rs6816247	0.82[CEU][hapmap]
rs6827500	0.89[ASN][1000 genomes]
rs6837581	0.89[ASN][1000 genomes]
rs6842783	0.89[ASN][1000 genomes]
rs6845623	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6848191	0.89[ASN][1000 genomes]
rs6848385	0.89[ASN][1000 genomes]
rs6850756	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6853904	0.85[ASN][1000 genomes]
rs72718440	0.89[ASN][1000 genomes]
rs72946978	0.89[ASN][1000 genomes]
rs7695458	0.82[CEU][hapmap]
rs7699731	0.82[CEU][hapmap]
rs9985602	0.91[ASN][1000 genomes]
rs9986085	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9995208	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9995231	0.87[ASN][1000 genomes]
rs9998887	0.89[ASN][1000 genomes]
rs9999736	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142990000-143051200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:143004600-143051600	Weak transcription	Pancreas	Pancrea
3	chr4:143010400-143057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:143018800-143109600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:143025400-143066800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:143030000-143057000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:143031000-143064800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:143034000-143061600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:143039200-143059000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:143040600-143049800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:143042200-143051400	Weak transcription	Aorta	Aorta
12	chr4:143042200-143060200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:143042600-143049800	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:143042600-143051600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:143043400-143089000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:143043600-143056600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:143043800-143054000	Weak transcription	Psoas Muscle	Psoas
18	chr4:143045400-143050200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:143045600-143050000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:143045800-143057200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:143046000-143049800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:143046000-143049800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:143046000-143049800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:143046000-143050200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr4:143046000-143050600	Weak transcription	HMEC	breast
26	chr4:143046000-143051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:143046000-143051600	Weak transcription	NHEK	skin
28	chr4:143046400-143051400	Weak transcription	Primary T cells from cord blood	blood
29	chr4:143046400-143052200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr4:143046400-143054600	Weak transcription	HSMM	muscle
31	chr4:143046800-143057200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:143047000-143049800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:143047200-143051200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:143047600-143049800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:143048000-143050200	Enhancers	Rectal Smooth Muscle	rectum
36	chr4:143048200-143049800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:143048400-143050000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:143048800-143051000	Weak transcription	Fetal Intestine Small	intestine
39	chr4:143049000-143050200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:143049000-143050400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr4:143049000-143050400	Strong transcription	HSMMtube	muscle
42	chr4:143049400-143049800	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:143049400-143050600	Enhancers	Fetal Lung	lung
44	chr4:143049400-143050600	Enhancers	Left Ventricle	heart
45	chr4:143049400-143051400	Enhancers	HUVEC	blood vessel
46	chr4:143049400-143051800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr4:143049400-143052200	Enhancers	Fetal Heart	heart
48	chr4:143049600-143049800	Enhancers	Right Ventricle	heart
49	chr4:143049600-143050000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:143049600-143050000	Enhancers	Fetal Muscle Leg	muscle

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