Variant report

Variant	rs13132859
Chromosome Location	chr4:53982039-53982040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1038354	0.83[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10517276	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10517283	1.00[JPT][hapmap]
rs12641339	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13104284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13112198	0.87[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13113235	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13114411	0.85[CEU][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13117887	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13118564	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13119115	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13119284	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13120634	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13122232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13123149	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13123263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13140090	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141532	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13143381	0.90[CEU][hapmap]
rs13151227	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13152478	0.86[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17082362	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17703292	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs4103860	0.83[ASN][1000 genomes]
rs4398582	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864443	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864720	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864724	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822050	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7692586	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs922904	0.83[CEU][hapmap]
rs9312636	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9998819	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53965800-53986000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:53968400-53983200	Weak transcription	NHEK	skin
3	chr4:53968400-53984600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:53969200-53983200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:53978800-54008000	Weak transcription	Primary T cells from cord blood	blood
6	chr4:53979600-53982600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:53979600-53983200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:53980000-53982800	Weak transcription	HMEC	breast
9	chr4:53980000-53983000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:53980000-53983400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr4:53980000-53985400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:53980000-53985800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:53980000-53985800	Weak transcription	NHLF	lung
14	chr4:53980000-53986800	Weak transcription	Aorta	Aorta
15	chr4:53980400-53982600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:53980400-53985800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:53980400-53993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:53980600-53982600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:53980600-53982600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:53980600-53982600	Weak transcription	Osteobl	bone
21	chr4:53980800-53985600	Weak transcription	NHDF-Ad	bronchial
22	chr4:53981200-53985800	Weak transcription	Fetal Lung	lung
23	chr4:53981800-53985600	Weak transcription	Fetal Intestine Small	intestine
24	chr4:53981800-53986000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:53982000-53982200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr4:53982000-53982800	Weak transcription	Ovary	ovary
27	chr4:53982000-53983200	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links