Variant report

Variant	rs11578400
Chromosome Location	chr1:92794031-92794032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10874637	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875349	0.90[ASN][1000 genomes]
rs11164226	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164288	0.90[ASN][1000 genomes]
rs11164312	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164546	0.90[ASN][1000 genomes]
rs11577572	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11577839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578012	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580693	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11585255	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586355	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11586989	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11588044	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588153	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11589858	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803457	0.90[ASN][1000 genomes]
rs12024731	0.90[ASN][1000 genomes]
rs12086394	0.90[ASN][1000 genomes]
rs12094293	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401372	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404806	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12406749	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12407622	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12411162	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12724638	0.89[ASN][1000 genomes]
rs12727665	1.00[ASN][1000 genomes]
rs12731923	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12735898	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740246	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12749317	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12753920	0.89[ASN][1000 genomes]
rs12755781	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757533	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12759512	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384612	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384613	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1487536	0.90[ASN][1000 genomes]
rs1542685	0.90[ASN][1000 genomes]
rs17519385	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17519972	0.89[ASN][1000 genomes]
rs17578686	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1809606	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004814	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069051	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391158	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391162	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103178	0.90[ASN][1000 genomes]
rs3131814	0.90[ASN][1000 genomes]
rs34090353	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35015161	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35580949	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3929737	0.90[ASN][1000 genomes]
rs4393167	0.90[ASN][1000 genomes]
rs4414050	0.90[ASN][1000 genomes]
rs4658294	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4658297	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4658298	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4658299	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4658300	0.90[ASN][1000 genomes]
rs4949888	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970699	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970713	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58394161	0.83[ASN][1000 genomes]
rs6603962	0.90[ASN][1000 genomes]
rs6603971	0.90[ASN][1000 genomes]
rs6603973	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6603974	0.83[ASN][1000 genomes]
rs6604088	0.90[ASN][1000 genomes]
rs6604090	0.90[ASN][1000 genomes]
rs6661384	0.90[ASN][1000 genomes]
rs6662379	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662920	0.84[EUR][1000 genomes]
rs6663118	0.81[ASN][1000 genomes]
rs6663278	0.90[ASN][1000 genomes]
rs6663905	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668803	0.90[ASN][1000 genomes]
rs66758257	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6702267	0.90[ASN][1000 genomes]
rs72720457	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733012	0.90[ASN][1000 genomes]
rs745793	0.90[ASN][1000 genomes]
rs7511656	0.89[ASN][1000 genomes]
rs7511669	0.89[ASN][1000 genomes]
rs7517541	0.90[ASN][1000 genomes]
rs7518974	0.90[ASN][1000 genomes]
rs7520275	0.90[ASN][1000 genomes]
rs7522081	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7524120	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539757	0.90[ASN][1000 genomes]
rs7543947	0.90[ASN][1000 genomes]
rs7550680	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9439911	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943178	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised 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	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv871352	chr1:92761127-92807238	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv870854	chr1:92765102-92807238	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv871387	chr1:92765102-92813741	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92765800-92850000	Weak transcription	Small Intestine	intestine
2	chr1:92771800-92794800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:92771800-92823800	Weak transcription	Colonic Mucosa	Colon
4	chr1:92773000-92800800	Weak transcription	NHDF-Ad	bronchial
5	chr1:92778000-92799200	Weak transcription	Hela-S3	cervix
6	chr1:92782200-92803400	Weak transcription	Stomach Mucosa	stomach
7	chr1:92784400-92808200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:92789600-92796000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:92789800-92812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:92789800-92830600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:92790000-92794400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:92790000-92815200	Weak transcription	Psoas Muscle	Psoas
13	chr1:92790400-92794600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:92790400-92797800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:92790400-92803600	Weak transcription	HUVEC	blood vessel
16	chr1:92790800-92802200	Weak transcription	HepG2	liver
17	chr1:92791200-92795800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr1:92791400-92794200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:92791400-92794200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr1:92791400-92794200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr1:92791400-92795400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:92791400-92795800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
23	chr1:92791600-92794600	ZNF genes & repeats	Fetal Lung	lung
24	chr1:92791600-92794800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
25	chr1:92791600-92795600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
26	chr1:92791600-92795800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:92791600-92796200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:92791600-92796600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr1:92792200-92795000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:92792400-92794400	Weak transcription	NH-A	brain
31	chr1:92792400-92794400	Weak transcription	NHEK	skin
32	chr1:92792400-92794600	Weak transcription	NHLF	lung
33	chr1:92792400-92794800	Weak transcription	Fetal Kidney	kidney
34	chr1:92792400-92795000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:92792400-92799000	Weak transcription	Osteobl	bone
36	chr1:92792400-92817400	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:92792400-92823600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:92792600-92794200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:92792600-92794200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr1:92792600-92794200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:92792600-92794200	Weak transcription	Fetal Intestine Small	intestine
42	chr1:92792600-92794400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:92792600-92794400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:92792600-92794400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:92792600-92794400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:92792600-92794400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:92792600-92794400	Weak transcription	Aorta	Aorta
48	chr1:92792600-92794400	Weak transcription	Esophagus	oesophagus
49	chr1:92792600-92794400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:92792600-92794400	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links