Variant report

Variant	rs62309402
Chromosome Location	chr4:48331520-48331521
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48322582..48327982-chr4:48329571..48333922,4	K562	blood:
2	chr4:48331436..48334148-chr4:48342438..48345400,3	MCF-7	breast:
3	chr4:48330630..48332591-chr4:48335471..48337148,2	K562	blood:
4	chr4:48329154..48338368-chr4:48340296..48348694,15	MCF-7	breast:
5	chr4:48322582..48325559-chr4:48331467..48333922,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11723080	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11947400	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2271265	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs309868	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs309870	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs309871	0.88[ASN][1000 genomes]
rs309873	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs309875	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs309887	0.96[EUR][1000 genomes]
rs418214	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4695369	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55784928	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55860639	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62309366	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62309367	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62309371	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62309372	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62309393	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62309398	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62309399	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62309400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62309401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62311483	0.83[AMR][1000 genomes]
rs6833004	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48325200-48334200	Weak transcription	Placenta	Placenta
2	chr4:48329800-48331800	Enhancers	HSMMtube	muscle
3	chr4:48330000-48334200	Enhancers	HSMM	muscle
4	chr4:48330000-48336200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
6	chr4:48330200-48335200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:48330400-48333800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:48330600-48332000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr4:48330800-48336000	Enhancers	NHDF-Ad	bronchial
10	chr4:48331000-48331600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr4:48331000-48331600	Enhancers	HepG2	liver
12	chr4:48331000-48331800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:48331000-48331800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:48331000-48331800	Enhancers	Liver	Liver
15	chr4:48331000-48332200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:48331000-48334200	Enhancers	NH-A	brain
17	chr4:48331000-48334200	Enhancers	NHLF	lung
18	chr4:48331000-48336400	Enhancers	NHEK	skin
19	chr4:48331000-48337400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:48331200-48331600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:48331200-48331600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:48331200-48331600	Enhancers	Fetal Intestine Small	intestine
23	chr4:48331200-48331600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr4:48331200-48331600	Enhancers	Small Intestine	intestine
25	chr4:48331200-48331600	Enhancers	K562	blood
26	chr4:48331200-48331800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:48331200-48332200	Enhancers	A549	lung
28	chr4:48331200-48333000	Enhancers	Hela-S3	cervix
29	chr4:48331200-48334200	Enhancers	Osteobl	bone
30	chr4:48331200-48335000	Enhancers	HMEC	breast
31	chr4:48331200-48336400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:48331400-48331600	Enhancers	Stomach Mucosa	stomach
33	chr4:48331400-48331800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:48331400-48331800	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr4:48331400-48332800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:48331400-48332800	Enhancers	HUVEC	blood vessel
37	chr4:48331400-48334200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links