Variant report

Variant	rs28508082
Chromosome Location	chr4:53785560-53785561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53784136..53787451-chr4:53789900..53792268,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10004829	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014061	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014144	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030623	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10034233	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049923	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331609	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167293	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698672	0.83[ASN][1000 genomes]
rs2086727	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2200225	0.83[ASN][1000 genomes]
rs28432778	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472535	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28491101	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564509	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28610009	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615713	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28678012	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28690295	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28786135	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930104	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930105	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930106	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301096	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301098	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301099	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301103	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301104	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301113	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301114	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301116	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443054	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458513	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833350	0.83[ASN][1000 genomes]
rs6855240	0.83[ASN][1000 genomes]
rs7658319	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677726	0.83[ASN][1000 genomes]
rs7680614	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996166	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9998405	1.00[EUR][1000 genomes];1.00[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	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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
2	chr4:53734600-53822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:53736600-53785600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:53761000-53788000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:53767600-53789000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:53768600-53788200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:53768800-53815600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:53769000-53804400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:53769600-53792000	Weak transcription	Lung	lung
10	chr4:53771000-53791600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:53773600-53787000	Weak transcription	Dnd41	blood
12	chr4:53774600-53798400	Weak transcription	HSMMtube	muscle
13	chr4:53780800-53786600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:53781400-53788600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:53781600-53791800	Weak transcription	Osteobl	bone
16	chr4:53782200-53791600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:53782200-53792400	Weak transcription	Pancreas	Pancrea
18	chr4:53782200-53799000	Weak transcription	NHLF	lung
19	chr4:53782400-53785800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:53782400-53786000	Weak transcription	HepG2	liver
21	chr4:53782400-53786400	Weak transcription	Fetal Lung	lung
22	chr4:53782400-53787400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:53782400-53790600	Weak transcription	Fetal Intestine Large	intestine
24	chr4:53782400-53791600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:53782400-53791800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:53782400-53792000	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:53782400-53794600	Weak transcription	Fetal Stomach	stomach
28	chr4:53782400-53797200	Weak transcription	Liver	Liver
29	chr4:53783000-53791800	Weak transcription	Stomach Mucosa	stomach
30	chr4:53783600-53786800	Strong transcription	Primary T cells from cord blood	blood
31	chr4:53784400-53787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:53784400-53791600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:53784400-53791600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:53785000-53785600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:53785000-53785600	Strong transcription	Primary B cells from cord blood	blood
36	chr4:53785000-53785600	Strong transcription	NHDF-Ad	bronchial
37	chr4:53785200-53785600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:53785200-53785600	Enhancers	NHEK	skin
39	chr4:53785200-53786200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:53785200-53791800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links