Variant report

Variant	rs59613864
Chromosome Location	chr21:17908346-17908347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr21:17907407-17909899	Hela-S3	cervix:	n/a	chr21:17908534-17908548 chr21:17908537-17908546

Variant related genes	Relation type
MIR99A	TF binding region
MIRLET7C	TF binding region
LINC00478	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10084583	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11910639	1.00[EUR][1000 genomes]
rs28566095	1.00[AMR][1000 genomes]
rs28750139	1.00[EUR][1000 genomes]
rs55725525	1.00[EUR][1000 genomes]
rs59398000	1.00[EUR][1000 genomes]
rs73369752	1.00[EUR][1000 genomes]
rs73891587	1.00[EUR][1000 genomes]
rs73891590	1.00[EUR][1000 genomes]
rs73891608	1.00[EUR][1000 genomes]
rs73891609	1.00[EUR][1000 genomes]
rs73891610	1.00[EUR][1000 genomes]
rs73891615	1.00[EUR][1000 genomes]
rs73891620	1.00[EUR][1000 genomes]
rs73891621	1.00[EUR][1000 genomes]
rs73891622	1.00[EUR][1000 genomes]
rs73891630	1.00[EUR][1000 genomes]
rs73891632	1.00[EUR][1000 genomes]
rs73893766	1.00[EUR][1000 genomes]
rs9974670	1.00[AMR][1000 genomes]
rs9980238	1.00[EUR][1000 genomes]
rs9982363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9983563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9983598	1.00[AMR][1000 genomes]
rs9983994	1.00[EUR][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	nsv1064857	chr21:17628760-18533131	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
2	nsv544382	chr21:17628760-18533131	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
3	esv3405994	chr21:17895130-17912420	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	292 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17904600-17914200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr21:17905600-17909200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
3	chr21:17905800-17910200	Active TSS	Brain Substantia Nigra	brain
4	chr21:17905800-17910600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr21:17905800-17910800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr21:17906000-17910000	Active TSS	Brain Cingulate Gyrus	brain
7	chr21:17906000-17910200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr21:17906000-17910200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr21:17906000-17910600	Active TSS	Ovary	ovary
10	chr21:17906000-17911000	Active TSS	Brain Angular Gyrus	brain
11	chr21:17906200-17910200	Active TSS	Brain Anterior Caudate	brain
12	chr21:17906200-17910200	Active TSS	Right Ventricle	heart
13	chr21:17906200-17910800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:17906200-17911000	Active TSS	NHLF	lung
15	chr21:17906200-17912000	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr21:17906400-17908400	Active TSS	Brain Hippocampus Middle	brain
17	chr21:17906400-17908600	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr21:17906400-17909600	Active TSS	Colon Smooth Muscle	Colon
19	chr21:17906400-17910000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr21:17906400-17910000	Active TSS	NHDF-Ad	bronchial
21	chr21:17906400-17910200	Active TSS	Psoas Muscle	Psoas
22	chr21:17906400-17912200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:17906400-17912400	Active TSS	Right Atrium	heart
24	chr21:17906600-17910200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr21:17906600-17910600	Active TSS	Fetal Lung	lung
26	chr21:17906600-17910600	Active TSS	HMEC	breast
27	chr21:17906600-17911400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr21:17906800-17912400	Active TSS	Fetal Brain Female	brain
29	chr21:17907000-17908400	Active TSS	NHEK	skin
30	chr21:17907000-17909800	Active TSS	Stomach Smooth Muscle	stomach
31	chr21:17907000-17910200	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr21:17907000-17910600	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr21:17907000-17911000	Active TSS	Brain Germinal Matrix	brain
34	chr21:17907000-17911000	Active TSS	HSMMtube	muscle
35	chr21:17907200-17908400	Active TSS	Osteobl	bone
36	chr21:17907200-17908800	Enhancers	HUVEC	blood vessel
37	chr21:17907200-17910000	Active TSS	Liver	Liver
38	chr21:17907200-17910800	Active TSS	Fetal Muscle Leg	muscle
39	chr21:17907200-17912200	Active TSS	Adipose Nuclei	Adipose
40	chr21:17907600-17909200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr21:17907600-17909200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr21:17907600-17909600	Enhancers	Fetal Kidney	kidney
43	chr21:17907600-17912000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr21:17907800-17908400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr21:17907800-17908600	Weak transcription	HSMM	muscle
46	chr21:17907800-17909200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr21:17907800-17909400	Weak transcription	Esophagus	oesophagus
48	chr21:17907800-17909400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr21:17907800-17909400	Weak transcription	Left Ventricle	heart
50	chr21:17907800-17911800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links