Variant report

Variant	rs533173
Chromosome Location	chr6:143115760-143115761
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11155264	0.82[ASN][1000 genomes]
rs197494	0.86[JPT][hapmap]
rs197496	0.86[JPT][hapmap]
rs197497	0.86[JPT][hapmap]
rs197511	0.86[JPT][hapmap]
rs2328388	0.83[ASN][1000 genomes]
rs472185	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs472288	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs473497	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs478768	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs487754	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491414	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491953	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs492156	0.88[ASN][1000 genomes]
rs494038	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs494954	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507404	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511565	0.86[ASN][1000 genomes]
rs512808	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs516300	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs519874	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs525928	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs527870	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs533117	0.83[ASN][1000 genomes]
rs541274	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs550149	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs552004	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs552928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557004	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs559818	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs561642	0.92[ASN][1000 genomes]
rs576657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs576760	0.82[ASN][1000 genomes]
rs9386009	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9403407	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830828	chr6:142970134-143116517	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 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	chr6:143095800-143117600	Weak transcription	Fetal Lung	lung
2	chr6:143095800-143122200	Weak transcription	NHEK	skin
3	chr6:143096000-143117800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:143096000-143122000	Weak transcription	Fetal Intestine Small	intestine
5	chr6:143096200-143120800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:143096200-143140800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:143103600-143117600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:143103600-143124800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:143103800-143125400	Weak transcription	Fetal Thymus	thymus
10	chr6:143105800-143121000	Weak transcription	Brain Angular Gyrus	brain
11	chr6:143105800-143140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:143106000-143118800	Weak transcription	Primary B cells from cord blood	blood
13	chr6:143106000-143128200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:143106000-143140400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:143106200-143116800	Weak transcription	GM12878-XiMat	blood
16	chr6:143108200-143121200	Weak transcription	HSMM	muscle
17	chr6:143108400-143119400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:143108800-143123600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:143109200-143117000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:143109200-143117600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:143109200-143121000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:143109400-143117000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:143111600-143117200	Weak transcription	Primary T cells from cord blood	blood
24	chr6:143112200-143117400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr6:143112200-143139400	Weak transcription	HepG2	liver
26	chr6:143112400-143117600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:143112600-143117600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:143113200-143119400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:143113200-143140400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:143113400-143116000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:143113400-143117000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:143113400-143117000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr6:143113800-143120800	Weak transcription	Pancreas	Pancrea
34	chr6:143114200-143140800	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:143114600-143115800	Enhancers	Fetal Brain Male	brain
36	chr6:143115000-143115800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr6:143115000-143116200	Enhancers	Fetal Brain Female	brain
38	chr6:143115400-143115800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr6:143115400-143116000	Enhancers	NHDF-Ad	bronchial
40	chr6:143115400-143116200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr6:143115600-143116000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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