Variant report

Variant	rs59580400
Chromosome Location	chr11:3964269-3964270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr11:3963648-3964328	HepG2	liver:	n/a	chr11:3963812-3963826
2	TCF7L2	chr11:3963692-3964397	HepG2	liver:	n/a	n/a
3	HNF4A	chr11:3963704-3964378	HepG2	liver:	n/a	chr11:3964197-3964209
4	FOXA2	chr11:3963632-3964271	HepG2	liver:	n/a	chr11:3963875-3963887
5	ARID3A	chr11:3963620-3964681	HepG2	liver:	n/a	n/a
6	FOXA2	chr11:3963150-3964464	HepG2	liver:	n/a	chr11:3963875-3963887

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3963150..3965730-chr11:3971154..3972718,2	K562	blood:
2	chr11:3959785..3962625-chr11:3963394..3965455,2	K562	blood:

Variant related genes	Relation type
STIM1	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10500591	0.85[AFR][1000 genomes]
rs11821399	1.00[AMR][1000 genomes]
rs11823158	0.85[AMR][1000 genomes]
rs11827535	0.85[AMR][1000 genomes]
rs11827750	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11827795	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16929611	0.85[AFR][1000 genomes]
rs2167562	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2167563	0.85[AFR][1000 genomes]
rs2412336	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57282641	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57292382	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57365434	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58151848	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58461583	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59108256	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59178256	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59842937	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59973839	0.85[AMR][1000 genomes]
rs60110100	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60462758	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61225070	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61355819	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61589687	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6578420	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6578421	1.00[EUR][1000 genomes]
rs6578435	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7109227	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7114373	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7117657	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7122796	1.00[AMR][1000 genomes]
rs7123124	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7128522	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72555753	1.00[EUR][1000 genomes]
rs7924332	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7926343	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7931280	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7938706	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7938862	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7939086	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7939090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7940292	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7940511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7941743	0.84[AFR][1000 genomes]
rs7942028	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7942271	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7943217	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7949898	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs894456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv896895	chr11:3942001-3972236	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 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	chr11:3950400-3972200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:3951200-3965400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:3951200-3967600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:3958800-3968000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr11:3960000-3967600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr11:3960200-3967600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:3961200-3964600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:3961400-3964400	Enhancers	Right Atrium	heart
10	chr11:3961400-3964800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:3961400-3965200	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr11:3961400-3968600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:3961400-3968600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:3961400-3969200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:3961600-3966400	Enhancers	NHDF-Ad	bronchial
16	chr11:3961600-3967600	Weak transcription	Brain Angular Gyrus	brain
17	chr11:3961600-3967800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:3961600-3968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:3961600-3968400	Weak transcription	NHEK	skin
20	chr11:3961600-3975200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:3961800-3965600	Weak transcription	NHLF	lung
22	chr11:3961800-3968000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:3962000-3965200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:3962000-3971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:3962000-3973400	Weak transcription	Ovary	ovary
26	chr11:3962400-3968000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr11:3962400-3968400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr11:3962600-3968200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:3963000-3964800	Enhancers	Right Ventricle	heart
30	chr11:3963000-3966400	Enhancers	Psoas Muscle	Psoas
31	chr11:3963000-3967000	Enhancers	Fetal Thymus	thymus
32	chr11:3963000-3968600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:3963000-3973200	Enhancers	Primary B cells from peripheral blood	blood
34	chr11:3963200-3964400	Flanking Active TSS	GM12878-XiMat	blood
35	chr11:3963200-3964800	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr11:3963200-3965400	Enhancers	Liver	Liver
37	chr11:3963200-3967800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr11:3963200-3968400	Enhancers	Primary hematopoietic stem cells	blood
39	chr11:3963400-3964400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:3963400-3964400	Enhancers	Aorta	Aorta
41	chr11:3963400-3964400	Enhancers	Lung	lung
42	chr11:3963400-3964400	Enhancers	A549	lung
43	chr11:3963400-3964600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:3963400-3964600	Enhancers	Colon Smooth Muscle	Colon
45	chr11:3963400-3964600	Enhancers	Stomach Smooth Muscle	stomach
46	chr11:3963400-3964600	Enhancers	Spleen	Spleen
47	chr11:3963400-3964600	Enhancers	K562	blood
48	chr11:3963400-3964800	Enhancers	Duodenum Mucosa	Duodenum
49	chr11:3963400-3965200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr11:3963400-3965200	Enhancers	Small Intestine	intestine

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