Variant report

Variant	rs28542213
Chromosome Location	chr4:89780985-89780986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10019681	0.81[EUR][1000 genomes]
rs10033824	0.91[EUR][1000 genomes]
rs12648534	0.81[EUR][1000 genomes]
rs28459962	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28529050	0.81[EUR][1000 genomes]
rs3806788	0.84[ASN][1000 genomes]
rs4693971	0.92[EUR][1000 genomes]
rs4693973	0.86[EUR][1000 genomes]
rs4693975	0.81[EUR][1000 genomes]
rs4693976	0.81[EUR][1000 genomes]
rs58281712	0.81[EUR][1000 genomes]
rs62308744	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62308745	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62308746	0.81[EUR][1000 genomes]
rs62310476	0.81[EUR][1000 genomes]
rs7668636	0.81[EUR][1000 genomes]
rs7687539	0.81[EUR][1000 genomes]
rs7695732	0.81[EUR][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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 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	chr4:89768800-89789400	Weak transcription	Fetal Intestine Small	intestine
2	chr4:89771000-89803200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:89773600-89784200	Weak transcription	Gastric	stomach
4	chr4:89778400-89782800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:89778800-89782200	Enhancers	Fetal Lung	lung
6	chr4:89779000-89781600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr4:89779400-89781400	Enhancers	Primary hematopoietic stem cells	blood
8	chr4:89779600-89781000	Enhancers	Adipose Nuclei	Adipose
9	chr4:89779600-89781400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:89779600-89781600	Enhancers	Primary B cells from cord blood	blood
11	chr4:89779600-89782200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:89779800-89781800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:89779800-89782400	Enhancers	Fetal Stomach	stomach
14	chr4:89780000-89781000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr4:89780000-89782000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:89780200-89781000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr4:89780200-89782000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:89780400-89781000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr4:89780400-89781000	Enhancers	Liver	Liver
20	chr4:89780400-89781000	Genic enhancers	Placenta	Placenta
21	chr4:89780400-89781000	Enhancers	Right Atrium	heart
22	chr4:89780400-89782000	Enhancers	Brain Anterior Caudate	brain
23	chr4:89780400-89782200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:89780400-89782200	Enhancers	Brain Hippocampus Middle	brain
25	chr4:89780400-89782200	Enhancers	Fetal Kidney	kidney
26	chr4:89780600-89781000	Enhancers	H9 Cell Line	embryonic stem cell
27	chr4:89780600-89782000	Enhancers	Stomach Smooth Muscle	stomach
28	chr4:89780800-89781000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:89780800-89781000	Enhancers	Duodenum Mucosa	Duodenum
30	chr4:89780800-89781200	Weak transcription	Brain Substantia Nigra	brain
31	chr4:89780800-89781600	Weak transcription	Ovary	ovary
32	chr4:89780800-89782200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr4:89780800-89782400	Enhancers	Rectal Smooth Muscle	rectum
34	chr4:89780800-89786000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:89780800-89786000	Weak transcription	NHDF-Ad	bronchial
36	chr4:89780800-89786000	Weak transcription	Osteobl	bone
37	chr4:89780800-89800600	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links