Variant report

Variant	rs2823861
Chromosome Location	chr21:17906124-17906125
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	POLR2A	chr21:17905908-17907251	U87	brain:	n/a	n/a
2	CEBPB	chr21:17906059-17907135	ECC-1	luminal epithelium:	n/a	n/a
3	FOXM1	chr21:17905669-17906421	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr21:17905996-17906416	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr21:17905939-17907243	U87	brain:	n/a	n/a
6	FOXA2	chr21:17905999-17906375	A549	lung:	n/a	n/a
7	MXI1	chr21:17905834-17908101	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr21:17905220-17906306	K562	blood:	n/a	n/a
9	FOXA2	chr21:17905876-17906309	A549	lung:	n/a	n/a
10	FOXA1	chr21:17905962-17906207	T-47D	breast:	n/a	n/a
11	POLR2A	chr21:17905908-17907245	U87	brain:	n/a	n/a
12	GATA2	chr21:17905982-17907770	SH-SY5Y	brain:	n/a	chr21:17907187-17907196 chr21:17907186-17907196 chr21:17907188-17907205 chr21:17907180-17907201 chr21:17907183-17907199

Variant related genes	Relation type
LINC00478	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12481827	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12482215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12482590	0.96[ASN][1000 genomes]
rs12482914	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12483358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12483744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16998685	1.00[EUR][1000 genomes]
rs16998758	1.00[EUR][1000 genomes]
rs16998890	1.00[EUR][1000 genomes]
rs2032286	1.00[EUR][1000 genomes]
rs2155622	1.00[EUR][1000 genomes]
rs2186870	1.00[EUR][1000 genomes]
rs2212561	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2404135	1.00[EUR][1000 genomes]
rs2823823	1.00[JPT][hapmap]
rs2823840	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823841	1.00[EUR][1000 genomes]
rs2823850	1.00[EUR][1000 genomes]
rs2823851	1.00[EUR][1000 genomes]
rs2823857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823858	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823860	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2823864	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28622187	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34151244	0.96[ASN][1000 genomes]
rs35805038	1.00[ASN][1000 genomes]
rs57039340	1.00[EUR][1000 genomes]
rs58981188	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59527462	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7279732	1.00[EUR][1000 genomes]
rs73363436	0.96[ASN][1000 genomes]
rs73367422	0.96[ASN][1000 genomes]
rs73367434	1.00[EUR][1000 genomes]
rs73367453	1.00[EUR][1000 genomes]
rs73367470	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73367472	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73367500	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129337	1.00[JPT][hapmap]
rs8129839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8132608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8133774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8134294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8134648	1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975878	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9977113	0.96[ASN][1000 genomes]
rs9979076	0.81[AMR][1000 genomes];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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17894200-17906200	Weak transcription	Left Ventricle	heart
2	chr21:17894200-17906800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:17903600-17906800	Enhancers	HUVEC	blood vessel
4	chr21:17904000-17906600	Weak transcription	Fetal Kidney	kidney
5	chr21:17904400-17907400	Enhancers	Hela-S3	cervix
6	chr21:17904600-17906200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:17904600-17906200	Weak transcription	Esophagus	oesophagus
8	chr21:17904600-17906200	Enhancers	Fetal Lung	lung
9	chr21:17904600-17914200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:17905000-17906200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr21:17905000-17906200	Enhancers	Fetal Heart	heart
12	chr21:17905200-17906200	Enhancers	Colon Smooth Muscle	Colon
13	chr21:17905400-17906400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr21:17905400-17906400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr21:17905400-17906400	Flanking Active TSS	Fetal Brain Female	brain
16	chr21:17905400-17906600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr21:17905400-17906800	Flanking Active TSS	A549	lung
18	chr21:17905400-17907200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr21:17905600-17906200	Enhancers	NHLF	lung
20	chr21:17905600-17906400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr21:17905600-17906600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr21:17905600-17906600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr21:17905600-17907800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr21:17905600-17909200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr21:17905800-17906600	Enhancers	Fetal Stomach	stomach
26	chr21:17905800-17906600	Active TSS	Stomach Smooth Muscle	stomach
27	chr21:17905800-17910200	Active TSS	Brain Substantia Nigra	brain
28	chr21:17905800-17910600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr21:17905800-17910800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr21:17906000-17906200	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr21:17906000-17906200	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr21:17906000-17906200	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr21:17906000-17906200	Active TSS	HSMM	muscle
34	chr21:17906000-17906400	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr21:17906000-17906400	Flanking Active TSS	Fetal Brain Male	brain
36	chr21:17906000-17906400	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr21:17906000-17906400	Flanking Active TSS	Psoas Muscle	Psoas
38	chr21:17906000-17906400	Flanking Active TSS	Right Atrium	heart
39	chr21:17906000-17906400	Flanking Active TSS	HSMMtube	muscle
40	chr21:17906000-17906400	Flanking Active TSS	NHDF-Ad	bronchial
41	chr21:17906000-17906600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr21:17906000-17906600	Enhancers	Liver	Liver
43	chr21:17906000-17906600	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr21:17906000-17906800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr21:17906000-17907000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr21:17906000-17907200	Flanking Active TSS	Osteobl	bone
47	chr21:17906000-17908000	Flanking Active TSS	NH-A	brain
48	chr21:17906000-17910000	Active TSS	Brain Cingulate Gyrus	brain
49	chr21:17906000-17910200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr21:17906000-17910200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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