Variant report

Variant	rs9489490
Chromosome Location	chr6:118986996-118986997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:118985895..118989345-chr6:119015029..119017625,3	K562	blood:
2	chr6:118985710..118987649-chr6:118989150..118991916,2	K562	blood:
3	chr6:118977517..118980348-chr6:118986192..118988530,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10080340	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10155773	0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10214801	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10457339	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10457340	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10457346	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11153749	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11153762	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12190964	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12191005	0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12191529	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12191962	0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12192532	0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12197348	0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12199189	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12199190	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12200660	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12201928	1.00[EUR][1000 genomes]
rs12202466	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12202932	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12204374	0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12205793	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12206369	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12206459	0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12207554	0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12209500	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12209566	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12211934	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12212089	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12213494	1.00[EUR][1000 genomes]
rs12215364	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12215456	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12215565	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12215706	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13328242	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13437148	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13437314	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60500545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6903291	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6903632	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6904070	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6904344	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6934770	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6939873	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7743702	0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7755203	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7759420	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs7764014	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9320657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9320659	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9320661	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9320662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9372510	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9387582	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9398488	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9481810	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs9481812	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9481818	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9481822	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481823	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481824	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481829	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481830	0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481835	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481839	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489408	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9489410	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9489415	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9489422	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9489427	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489430	0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489434	0.82[YRI][hapmap];0.96[AFR][1000 genomes]
rs9489435	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489451	0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489464	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489468	0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489472	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489480	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489481	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489484	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489485	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489488	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489492	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489495	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9489496	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9489501	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9489505	0.85[YRI][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1025456	chr6:118669672-119058789	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv432958	chr6:118692307-119010307	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1034448	chr6:118698169-119016383	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1025097	chr6:118699752-119058789	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
11	nsv532052	chr6:118711850-119057295	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv432959	chr6:118716318-119010307	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv604556	chr6:118722589-119065365	Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv949416	chr6:118772508-119033063	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv604559	chr6:118786486-119113317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv1022865	chr6:118786586-119058789	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
18	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118973400-118988800	Weak transcription	NH-A	brain
2	chr6:118973600-118989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:118978200-118989800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:118981600-118988800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:118981600-118989600	Weak transcription	Left Ventricle	heart
6	chr6:118981800-118988000	Weak transcription	Fetal Lung	lung
7	chr6:118982000-118989000	Weak transcription	K562	blood
8	chr6:118983600-118990200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:118985200-118987000	Enhancers	Primary B cells from peripheral blood	blood
10	chr6:118985200-118987200	Enhancers	Stomach Mucosa	stomach
11	chr6:118985800-118989400	Weak transcription	Small Intestine	intestine
12	chr6:118986000-118987000	Enhancers	Primary T cells from cord blood	blood
13	chr6:118986000-118989400	Weak transcription	Adipose Nuclei	Adipose
14	chr6:118986200-118988000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr6:118986200-118988200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:118986400-118987000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr6:118986400-118987000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr6:118986400-118987200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:118986400-118987200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:118986400-118987200	Enhancers	Osteobl	bone
21	chr6:118986400-118987800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:118986400-118988200	Weak transcription	NHLF	lung
23	chr6:118986400-118988400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:118986400-118988400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:118986400-118988400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr6:118986400-118988600	Weak transcription	NHDF-Ad	bronchial
27	chr6:118986400-118988800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:118986400-118988800	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:118986400-118988800	Weak transcription	HSMM	muscle
30	chr6:118986400-118989000	Weak transcription	Dnd41	blood
31	chr6:118986400-118989000	Weak transcription	HSMMtube	muscle
32	chr6:118986400-118989400	Weak transcription	Primary B cells from cord blood	blood
33	chr6:118986400-118989400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:118986400-118989400	Weak transcription	Thymus	Thymus
35	chr6:118986400-118989600	Weak transcription	Fetal Thymus	thymus
36	chr6:118986400-118990000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr6:118986400-118990200	Weak transcription	HMEC	breast
38	chr6:118986400-118990400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:118986400-118991400	Enhancers	Psoas Muscle	Psoas
40	chr6:118986400-118991800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:118986400-118992200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:118986400-118992400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:118986400-118992400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr6:118986400-118994800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr6:118986400-118995000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:118986400-118995400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr6:118986400-119001800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:118986800-118990000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr6:118986800-118990800	Weak transcription	Gastric	stomach

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