Variant report

Variant	rs16999453
Chromosome Location	chr21:17906220-17906221
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	GATA3	chr21:17906177-17906252	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr21:17905908-17907251	U87	brain:	n/a	n/a
3	CEBPB	chr21:17906059-17907135	ECC-1	luminal epithelium:	n/a	n/a
4	FOXM1	chr21:17905669-17906421	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr21:17905996-17906416	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr21:17905939-17907243	U87	brain:	n/a	n/a
7	FOXA2	chr21:17905999-17906375	A549	lung:	n/a	n/a
8	MXI1	chr21:17905834-17908101	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr21:17905220-17906306	K562	blood:	n/a	n/a
10	FOXA2	chr21:17905876-17906309	A549	lung:	n/a	n/a
11	NFIC	chr21:17906156-17907855	ECC-1	luminal epithelium:	n/a	chr21:17907136-17907152 chr21:17907136-17907153
12	POLR2A	chr21:17905908-17907245	U87	brain:	n/a	n/a
13	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: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11910443	1.00[EUR][1000 genomes]
rs11910489	1.00[EUR][1000 genomes]
rs11911281	1.00[EUR][1000 genomes]
rs16998528	1.00[EUR][1000 genomes]
rs16998825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16998890	0.83[AMR][1000 genomes]
rs16999201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16999221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16999403	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16999411	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17000077	1.00[EUR][1000 genomes]
rs17000181	1.00[EUR][1000 genomes]
rs17000784	1.00[EUR][1000 genomes]
rs2032286	0.83[AMR][1000 genomes]
rs2243706	1.00[EUR][1000 genomes]
rs2823935	1.00[EUR][1000 genomes]
rs4380331	1.00[EUR][1000 genomes]
rs57784792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58347042	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6517701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6517702	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7275723	1.00[EUR][1000 genomes]
rs7277099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7277211	1.00[EUR][1000 genomes]
rs73367454	1.00[EUR][1000 genomes]
rs73367494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73369729	1.00[EUR][1000 genomes]
rs73893739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8127360	1.00[EUR][1000 genomes]
rs8128705	1.00[EUR][1000 genomes]
rs8128729	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8129493	1.00[EUR][1000 genomes]
rs8129644	1.00[EUR][1000 genomes]
rs8130130	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8131413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8131420	1.00[EUR][1000 genomes]
rs8132247	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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17894200-17906800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:17903600-17906800	Enhancers	HUVEC	blood vessel
3	chr21:17904000-17906600	Weak transcription	Fetal Kidney	kidney
4	chr21:17904400-17907400	Enhancers	Hela-S3	cervix
5	chr21:17904600-17914200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr21:17905400-17906400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr21:17905400-17906400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
8	chr21:17905400-17906400	Flanking Active TSS	Fetal Brain Female	brain
9	chr21:17905400-17906600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr21:17905400-17906800	Flanking Active TSS	A549	lung
11	chr21:17905400-17907200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr21:17905600-17906400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr21:17905600-17906600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr21:17905600-17906600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr21:17905600-17907800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr21:17905600-17909200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr21:17905800-17906600	Enhancers	Fetal Stomach	stomach
18	chr21:17905800-17906600	Active TSS	Stomach Smooth Muscle	stomach
19	chr21:17905800-17910200	Active TSS	Brain Substantia Nigra	brain
20	chr21:17905800-17910600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr21:17905800-17910800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr21:17906000-17906400	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr21:17906000-17906400	Flanking Active TSS	Fetal Brain Male	brain
24	chr21:17906000-17906400	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr21:17906000-17906400	Flanking Active TSS	Psoas Muscle	Psoas
26	chr21:17906000-17906400	Flanking Active TSS	Right Atrium	heart
27	chr21:17906000-17906400	Flanking Active TSS	HSMMtube	muscle
28	chr21:17906000-17906400	Flanking Active TSS	NHDF-Ad	bronchial
29	chr21:17906000-17906600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr21:17906000-17906600	Enhancers	Liver	Liver
31	chr21:17906000-17906600	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr21:17906000-17906800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr21:17906000-17907000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr21:17906000-17907200	Flanking Active TSS	Osteobl	bone
35	chr21:17906000-17908000	Flanking Active TSS	NH-A	brain
36	chr21:17906000-17910000	Active TSS	Brain Cingulate Gyrus	brain
37	chr21:17906000-17910200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr21:17906000-17910200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr21:17906000-17910600	Active TSS	Ovary	ovary
40	chr21:17906000-17911000	Active TSS	Brain Angular Gyrus	brain
41	chr21:17906200-17906400	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr21:17906200-17906400	Active TSS	Esophagus	oesophagus
43	chr21:17906200-17906400	Flanking Active TSS	Fetal Heart	heart
44	chr21:17906200-17906400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr21:17906200-17906400	Flanking Active TSS	HSMM	muscle
46	chr21:17906200-17906600	Flanking Active TSS	Fetal Lung	lung
47	chr21:17906200-17906600	Enhancers	Left Ventricle	heart
48	chr21:17906200-17906600	Enhancers	HMEC	breast
49	chr21:17906200-17907800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr21:17906200-17907800	Active TSS	Fetal Muscle Trunk	muscle

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