Variant report

Variant	rs17425479
Chromosome Location	chr4:124759620-124759621
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:124759565..124761746-chr4:124768373..124770897,2	MCF-7	breast:
2	chr4:124752778..124755449-chr4:124757344..124759853,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10518305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518306	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1368509	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17007484	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007499	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007509	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007553	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17425951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17491837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17492080	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4340803	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58148580	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58208464	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58498049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58530613	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6821590	0.80[ASN][1000 genomes]

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	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2754745	chr4:124698055-124770865	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17425479	TRPC3	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124743200-124759800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:124752400-124764800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:124752400-124769000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:124754800-124762800	Weak transcription	Aorta	Aorta
5	chr4:124755800-124761200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:124756000-124761000	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:124756600-124761400	Enhancers	NHDF-Ad	bronchial
8	chr4:124758000-124760400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:124758000-124760400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr4:124758400-124759800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:124758400-124761000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:124758400-124763400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:124758400-124769000	Weak transcription	Left Ventricle	heart
14	chr4:124758600-124761000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:124758600-124761000	Weak transcription	Fetal Stomach	stomach
16	chr4:124758600-124764000	Weak transcription	NH-A	brain
17	chr4:124758600-124765400	Weak transcription	Fetal Intestine Small	intestine
18	chr4:124759000-124761200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:124759200-124760000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:124759200-124760000	Enhancers	HUVEC	blood vessel
21	chr4:124759200-124762000	Enhancers	Fetal Lung	lung
22	chr4:124759400-124760000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:124759400-124760000	Enhancers	NHLF	lung
24	chr4:124759400-124760200	Enhancers	Fetal Muscle Leg	muscle
25	chr4:124759400-124760400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:124759400-124760600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr4:124759400-124761200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:124759600-124759800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:124759600-124759800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:124759600-124759800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:124759600-124759800	Enhancers	Ovary	ovary
32	chr4:124759600-124759800	Enhancers	Psoas Muscle	Psoas
33	chr4:124759600-124760000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr4:124759600-124760000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr4:124759600-124760000	Enhancers	Fetal Heart	heart
36	chr4:124759600-124760000	Enhancers	Stomach Mucosa	stomach
37	chr4:124759600-124760200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:124759600-124760200	Enhancers	HSMM	muscle
39	chr4:124759600-124760400	Enhancers	HSMMtube	muscle
40	chr4:124759600-124761000	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links