Variant report

Variant	rs9654569
Chromosome Location	chr6:163876552-163876553
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10080505	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12523713	0.92[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12523978	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17176494	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4112651	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60332904	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6455905	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6901592	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6902608	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906081	0.90[EUR][1000 genomes]
rs6906275	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6906725	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6910323	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6914093	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6917030	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6928869	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6936927	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6937072	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6937097	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73013516	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73013528	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73013553	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73015316	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7748261	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7759606	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761090	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7770852	0.92[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9456868	0.91[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458821	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9458823	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458825	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458828	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458830	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458837	0.92[CEU][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458849	0.92[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458857	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458859	0.92[CEU][hapmap];0.94[EUR][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	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1017495	chr6:163856399-163981095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv523664	chr6:163858237-163907885	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
2	chr6:163845400-163877800	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:163848800-163878400	Weak transcription	Pancreas	Pancrea
4	chr6:163852000-163880000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:163858400-163876600	Weak transcription	Primary B cells from cord blood	blood
6	chr6:163859600-163876600	Weak transcription	HUVEC	blood vessel
7	chr6:163859600-163878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:163860200-163877800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:163860400-163876600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:163860800-163878400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:163860800-163880000	Weak transcription	Lung	lung
12	chr6:163862600-163878000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:163862800-163878600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:163863000-163876800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr6:163863000-163880200	Weak transcription	Esophagus	oesophagus
16	chr6:163863200-163879200	Weak transcription	Fetal Brain Male	brain
17	chr6:163863600-163876600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:163863600-163878400	Weak transcription	Primary T cells from cord blood	blood
19	chr6:163863600-163878800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:163863800-163877800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:163863800-163877800	Weak transcription	Placenta	Placenta
22	chr6:163863800-163878000	Weak transcription	HMEC	breast
23	chr6:163863800-163878200	Weak transcription	NHEK	skin
24	chr6:163863800-163878800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:163865000-163877000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:163865200-163881400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:163865400-163877800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:163865400-163877800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:163865400-163878600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:163865400-163878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:163865600-163876600	Weak transcription	K562	blood
32	chr6:163865600-163878000	Weak transcription	Fetal Kidney	kidney
33	chr6:163867000-163877000	Weak transcription	Psoas Muscle	Psoas
34	chr6:163867800-163876600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:163868000-163876600	Weak transcription	Right Ventricle	heart
36	chr6:163869400-163876600	Weak transcription	HepG2	liver
37	chr6:163869400-163877600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:163869800-163878600	Weak transcription	Ovary	ovary
39	chr6:163870400-163876600	Weak transcription	Fetal Lung	lung
40	chr6:163870600-163876600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:163870800-163876800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:163870800-163878000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:163871200-163877400	Weak transcription	Adipose Nuclei	Adipose
44	chr6:163872000-163878800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:163872200-163877000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:163872200-163878400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr6:163872200-163880000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:163872400-163877600	Weak transcription	GM12878-XiMat	blood
49	chr6:163872400-163878400	Weak transcription	Gastric	stomach
50	chr6:163872800-163877800	Weak transcription	Small Intestine	intestine

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