Variant report

Variant	rs346475
Chromosome Location	chr4:86900011-86900012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11724681	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs168308	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs173201	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs182961	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2164535	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2164536	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2164537	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2575680	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589504	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589509	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2665877	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346467	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346471	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346480	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346484	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346485	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346488	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346492	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346498	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs346502	0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs346503	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs346504	0.91[CEU][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs346505	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs346506	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346507	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35158998	0.84[AMR][1000 genomes]
rs6851229	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs958860	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs958861	0.87[AMR][1000 genomes];0.88[EUR][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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
2	chr4:86863600-86902000	Weak transcription	Pancreas	Pancrea
3	chr4:86875200-86915800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:86880600-86915800	Weak transcription	Gastric	stomach
5	chr4:86885000-86915600	Weak transcription	Fetal Lung	lung
6	chr4:86887600-86915600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:86888800-86919200	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:86889400-86915800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:86889400-86935000	Weak transcription	Psoas Muscle	Psoas
10	chr4:86889600-86904000	Weak transcription	Aorta	Aorta
11	chr4:86890400-86901800	Weak transcription	Liver	Liver
12	chr4:86890400-86916000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:86891400-86915800	Weak transcription	HSMMtube	muscle
14	chr4:86891800-86905400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:86892000-86901400	Weak transcription	Fetal Kidney	kidney
16	chr4:86892000-86904000	Weak transcription	Adipose Nuclei	Adipose
17	chr4:86892000-86915600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:86892000-86915600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:86892000-86915800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:86892000-86916000	Weak transcription	Spleen	Spleen
21	chr4:86893000-86906600	Strong transcription	HUVEC	blood vessel
22	chr4:86893200-86906600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:86893200-86908600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:86894000-86907400	Weak transcription	Osteobl	bone
25	chr4:86894400-86900400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:86894400-86901800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:86894400-86901800	Weak transcription	Fetal Muscle Leg	muscle
28	chr4:86894400-86915800	Weak transcription	Ovary	ovary
29	chr4:86895000-86910400	Strong transcription	Primary B cells from cord blood	blood
30	chr4:86895400-86903800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:86896400-86900400	Strong transcription	NHDF-Ad	bronchial
32	chr4:86896600-86902600	Weak transcription	Fetal Stomach	stomach
33	chr4:86897000-86906800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:86897600-86915600	Weak transcription	Placenta	Placenta
35	chr4:86897600-86916000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:86897600-86916400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:86897800-86906800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:86898200-86900200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:86898600-86901600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:86899200-86902400	Weak transcription	HSMM	muscle
41	chr4:86899200-86927000	Weak transcription	Lung	lung
42	chr4:86899800-86915800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:86899800-86915800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr4:86899800-86917800	Weak transcription	Small Intestine	intestine
45	chr4:86900000-86915600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr4:86900000-86915800	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links