Variant report

Variant	rs71317821
Chromosome Location	chr3:23296397-23296398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12106681	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13060112	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13060251	0.85[EUR][1000 genomes]
rs13063185	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13067514	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13073761	0.93[AMR][1000 genomes]
rs13078970	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13084250	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13087238	0.93[AMR][1000 genomes]
rs13087563	0.85[EUR][1000 genomes]
rs13090633	0.84[EUR][1000 genomes]
rs13092830	0.81[EUR][1000 genomes]
rs13099586	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13100605	0.85[EUR][1000 genomes]
rs34259979	0.81[EUR][1000 genomes]
rs34443476	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34474308	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34504120	0.87[AMR][1000 genomes]
rs34513914	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34584255	0.85[EUR][1000 genomes]
rs34619482	0.93[AMR][1000 genomes]
rs34743949	0.82[EUR][1000 genomes]
rs34894979	0.81[AMR][1000 genomes]
rs34916096	0.81[AMR][1000 genomes]
rs34928966	0.81[AMR][1000 genomes]
rs35096750	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35218978	0.81[AMR][1000 genomes]
rs35230557	0.82[AMR][1000 genomes]
rs35240920	0.85[EUR][1000 genomes]
rs35245309	0.81[AMR][1000 genomes]
rs35266274	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35314441	0.81[AMR][1000 genomes]
rs35346188	0.85[EUR][1000 genomes]
rs35402533	0.82[EUR][1000 genomes]
rs35408638	0.81[AMR][1000 genomes]
rs35587590	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35649850	0.81[AMR][1000 genomes]
rs35776486	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35869522	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35892300	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35902312	0.93[AMR][1000 genomes]
rs35907941	0.81[AMR][1000 genomes]
rs35928592	0.82[AMR][1000 genomes]
rs36060079	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36123979	0.85[EUR][1000 genomes]
rs36124326	0.81[AMR][1000 genomes]
rs71317817	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71317819	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71317820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71317822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71317823	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71317824	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71317827	0.85[EUR][1000 genomes]
rs71317829	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71322171	0.82[EUR][1000 genomes]
rs71322174	0.81[AMR][1000 genomes]
rs71322184	0.81[AMR][1000 genomes]
rs71322187	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23274800-23298200	Weak transcription	Aorta	Aorta
2	chr3:23281400-23298200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:23283600-23302200	Weak transcription	Left Ventricle	heart
4	chr3:23290600-23298200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:23291600-23298400	Weak transcription	Spleen	Spleen
6	chr3:23291800-23298200	Weak transcription	Thymus	Thymus
7	chr3:23292200-23298800	Weak transcription	Primary T cells from cord blood	blood
8	chr3:23292800-23298400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:23292800-23304200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:23292800-23306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:23293000-23298600	Weak transcription	Osteobl	bone
12	chr3:23293000-23303800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:23293200-23299400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:23293600-23298200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:23294400-23296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:23294400-23297000	Enhancers	Primary B cells from cord blood	blood
17	chr3:23294800-23297600	Enhancers	Liver	Liver
18	chr3:23294800-23299200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr3:23295000-23296800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:23295000-23298400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:23295200-23297800	Enhancers	GM12878-XiMat	blood
22	chr3:23295200-23298200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:23295200-23321800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:23295400-23296400	Enhancers	Brain Angular Gyrus	brain
25	chr3:23295400-23296600	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:23295600-23296400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr3:23295600-23296400	Enhancers	Brain Anterior Caudate	brain
28	chr3:23295600-23296400	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:23295600-23296400	Enhancers	Brain Substantia Nigra	brain
30	chr3:23295600-23296400	Flanking Active TSS	A549	lung
31	chr3:23295800-23296400	Enhancers	Adipose Nuclei	Adipose
32	chr3:23295800-23296400	Enhancers	Fetal Kidney	kidney
33	chr3:23295800-23296400	Enhancers	Psoas Muscle	Psoas
34	chr3:23295800-23296400	Enhancers	Right Atrium	heart
35	chr3:23295800-23297000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:23296000-23298200	Weak transcription	Pancreas	Pancrea
37	chr3:23296000-23300600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:23296000-23302000	Weak transcription	Lung	lung
39	chr3:23296200-23296600	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr3:23296200-23296600	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:23296200-23296600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr3:23296200-23296800	Enhancers	Fetal Thymus	thymus
43	chr3:23296200-23297600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:23296200-23297600	Weak transcription	Brain Hippocampus Middle	brain

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