Variant report

Variant	rs887515
Chromosome Location	chr3:52523405-52523406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011064	1.00[JPT][hapmap]
rs1077142	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs10865972	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11705963	0.86[EUR][1000 genomes]
rs11706108	0.86[EUR][1000 genomes]
rs11707864	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs11707931	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs11709658	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs11711934	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs11714402	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11716017	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs11718125	0.87[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11721286	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs123598	1.00[JPT][hapmap]
rs123602	0.93[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs123603	1.00[JPT][hapmap]
rs13059674	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs13060192	1.00[JPT][hapmap]
rs13075370	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap]
rs13076890	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs13091360	1.00[JPT][hapmap]
rs13091545	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs1541495	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17052058	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs17052061	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs17052068	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2016575	0.87[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs2109558	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2109559	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2159607	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2215466	1.00[JPT][hapmap]
rs2335640	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs28481563	0.86[EUR][1000 genomes]
rs2878549	1.00[JPT][hapmap]
rs34238085	0.82[EUR][1000 genomes]
rs34261027	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523877	0.82[EUR][1000 genomes]
rs34762015	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs35860312	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs3774409	1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.87[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs390802	0.93[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs409803	1.00[JPT][hapmap]
rs419050	1.00[JPT][hapmap]
rs419604	1.00[JPT][hapmap]
rs419752	1.00[JPT][hapmap]
rs4312651	1.00[JPT][hapmap]
rs4687543	0.83[ASN][1000 genomes]
rs4687614	1.00[JPT][hapmap]
rs4687617	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4687618	1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[JPT][hapmap]
rs498946	0.93[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs55965068	0.80[EUR][1000 genomes]
rs55997317	0.80[EUR][1000 genomes]
rs57441156	0.80[EUR][1000 genomes]
rs613519	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs634382	0.80[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6445386	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs6445486	1.00[JPT][hapmap]
rs6445506	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs66462821	0.85[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap]
rs6763882	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap]
rs6784615	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6794675	0.82[EUR][1000 genomes]
rs6796333	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs6800707	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810027	1.00[JPT][hapmap]
rs728408	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs758803	1.00[JPT][hapmap]
rs7620015	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7643570	0.91[GIH][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs82825	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs887514	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs929528	1.00[JPT][hapmap]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[JPT][hapmap]
rs9861879	0.86[EUR][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS 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 target site	63 gene(s)	inside rSNPs	diseases
7	nsv590304	chr3:52517206-52529266	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
2	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:52498600-52527200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr3:52499400-52527800	Strong transcription	Primary T cells from cord blood	blood
9	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
11	chr3:52504200-52526600	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr3:52504200-52526800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:52504200-52527400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:52504200-52527400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:52504200-52527600	Strong transcription	Dnd41	blood
16	chr3:52504200-52527800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:52504200-52528000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:52504200-52528000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:52504200-52528600	Strong transcription	Brain Germinal Matrix	brain
20	chr3:52504400-52523600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:52504400-52523800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr3:52504400-52527400	Strong transcription	Osteobl	bone
23	chr3:52504400-52527600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:52504400-52527600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:52504400-52528000	Strong transcription	Fetal Brain Female	brain
26	chr3:52504800-52523800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr3:52504800-52527400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:52504800-52528000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:52505000-52527000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:52506200-52523600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:52506400-52527400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:52507400-52527800	Strong transcription	Fetal Thymus	thymus
33	chr3:52508000-52532200	Weak transcription	K562	blood
34	chr3:52509400-52528000	Strong transcription	Gastric	stomach
35	chr3:52509600-52528200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:52510000-52524200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:52510000-52526400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:52510200-52526200	Strong transcription	Pancreas	Pancrea
39	chr3:52510600-52528600	Weak transcription	Fetal Brain Male	brain
40	chr3:52511400-52528000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:52513000-52523800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:52513400-52541400	Weak transcription	A549	lung
43	chr3:52513600-52530000	Weak transcription	Fetal Kidney	kidney
44	chr3:52514600-52523800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:52514600-52534200	Weak transcription	Small Intestine	intestine
46	chr3:52514800-52523600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:52515600-52528400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:52516200-52524000	Strong transcription	Liver	Liver
49	chr3:52516200-52526000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:52517200-52528200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links