Variant report

Variant	rs346472
Chromosome Location	chr4:86907146-86907147
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs189395	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs189396	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2043647	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2136782	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2164538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2575681	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2575682	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589505	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589510	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2665869	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2665876	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346469	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346470	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346476	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346477	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346482	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346483	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs346486	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346487	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346489	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346490	0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346491	0.84[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346493	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346494	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346495	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346496	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346499	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs346501	1.00[JPT][hapmap]
rs62305515	0.82[ASN][1000 genomes]
rs62305516	0.82[ASN][1000 genomes]
rs62305518	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1005257	chr4:86899596-86925469	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
2	chr4:86875200-86915800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:86880600-86915800	Weak transcription	Gastric	stomach
4	chr4:86885000-86915600	Weak transcription	Fetal Lung	lung
5	chr4:86887600-86915600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:86888800-86919200	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:86889400-86915800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:86889400-86935000	Weak transcription	Psoas Muscle	Psoas
9	chr4:86890400-86916000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:86891400-86915800	Weak transcription	HSMMtube	muscle
11	chr4:86892000-86915600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:86892000-86915600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:86892000-86915800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:86892000-86916000	Weak transcription	Spleen	Spleen
15	chr4:86893200-86908600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr4:86894000-86907400	Weak transcription	Osteobl	bone
17	chr4:86894400-86915800	Weak transcription	Ovary	ovary
18	chr4:86895000-86910400	Strong transcription	Primary B cells from cord blood	blood
19	chr4:86897600-86915600	Weak transcription	Placenta	Placenta
20	chr4:86897600-86916000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:86897600-86916400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:86899200-86927000	Weak transcription	Lung	lung
23	chr4:86899800-86915800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:86899800-86915800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:86899800-86917800	Weak transcription	Small Intestine	intestine
26	chr4:86900000-86915600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr4:86900000-86915800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:86900200-86915800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:86901000-86915800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:86901600-86915800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:86902200-86915800	Weak transcription	Pancreas	Pancrea
32	chr4:86902800-86915800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:86902800-86915800	Weak transcription	Liver	Liver
34	chr4:86903000-86914600	Weak transcription	NHDF-Ad	bronchial
35	chr4:86904200-86912400	Weak transcription	Adipose Nuclei	Adipose
36	chr4:86904200-86915800	Weak transcription	Aorta	Aorta
37	chr4:86904200-86915800	Weak transcription	Fetal Stomach	stomach
38	chr4:86905000-86915800	Weak transcription	Fetal Kidney	kidney
39	chr4:86905000-86915800	Weak transcription	Right Ventricle	heart
40	chr4:86905600-86912200	Weak transcription	HSMM	muscle
41	chr4:86906000-86913200	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:86906400-86916000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:86906600-86907400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:86906600-86908600	Weak transcription	HUVEC	blood vessel
45	chr4:86906800-86913000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:86906800-86913200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:86906800-86913400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:86907000-86911000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links