Variant report

Variant	rs2823860
Chromosome Location	chr21:17905930-17905931
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	FOXM1	chr21:17905669-17906421	ECC-1	luminal epithelium:	n/a	n/a
3	MXI1	chr21:17905834-17908101	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr21:17905220-17906306	K562	blood:	n/a	n/a
5	FOXA2	chr21:17905876-17906309	A549	lung:	n/a	n/a
6	POLR2A	chr21:17905908-17907245	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17903700..17906085-chr21:17908034..17909928,2	K562	blood:

Variant related genes	Relation type
LINC00478	TF binding region
ENSG00000215386	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10084567	1.00[EUR][1000 genomes]
rs10084608	1.00[EUR][1000 genomes]
rs10084612	1.00[EUR][1000 genomes]
rs12481827	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12482215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12482590	0.96[ASN][1000 genomes]
rs12482914	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483358	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12483622	1.00[EUR][1000 genomes]
rs12483744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2040142	1.00[EUR][1000 genomes]
rs2212561	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2212562	1.00[EUR][1000 genomes]
rs2226435	1.00[EUR][1000 genomes]
rs2823821	1.00[EUR][1000 genomes]
rs2823822	1.00[EUR][1000 genomes]
rs2823823	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2823825	1.00[EUR][1000 genomes]
rs2823826	1.00[EUR][1000 genomes]
rs2823827	1.00[EUR][1000 genomes]
rs2823828	1.00[EUR][1000 genomes]
rs2823829	1.00[CHB][hapmap]
rs2823830	1.00[EUR][1000 genomes]
rs2823831	1.00[EUR][1000 genomes]
rs2823834	1.00[EUR][1000 genomes]
rs2823835	1.00[EUR][1000 genomes]
rs2823840	0.96[ASN][1000 genomes]
rs2823853	1.00[EUR][1000 genomes]
rs2823854	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2823855	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2823857	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2823858	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2823859	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2823861	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2823864	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2823866	1.00[EUR][1000 genomes]
rs28496427	1.00[EUR][1000 genomes]
rs28622187	0.96[ASN][1000 genomes]
rs28875621	1.00[EUR][1000 genomes]
rs2896759	1.00[EUR][1000 genomes]
rs2896760	1.00[EUR][1000 genomes]
rs34151244	0.96[ASN][1000 genomes]
rs35805038	1.00[ASN][1000 genomes]
rs57523013	1.00[EUR][1000 genomes]
rs58072187	1.00[EUR][1000 genomes]
rs58175294	1.00[EUR][1000 genomes]
rs58304651	1.00[EUR][1000 genomes]
rs58640456	1.00[EUR][1000 genomes]
rs58981188	0.96[ASN][1000 genomes]
rs60754236	1.00[EUR][1000 genomes]
rs7277815	1.00[EUR][1000 genomes]
rs7278273	1.00[EUR][1000 genomes]
rs7280438	1.00[EUR][1000 genomes]
rs7283241	1.00[EUR][1000 genomes]
rs7283307	1.00[EUR][1000 genomes]
rs7283311	1.00[EUR][1000 genomes]
rs73363406	1.00[EUR][1000 genomes]
rs73363409	1.00[EUR][1000 genomes]
rs73363411	1.00[EUR][1000 genomes]
rs73363436	0.96[ASN][1000 genomes]
rs73366681	1.00[EUR][1000 genomes]
rs73366695	1.00[EUR][1000 genomes]
rs73367422	0.96[ASN][1000 genomes]
rs73367470	0.96[ASN][1000 genomes]
rs73367472	0.96[ASN][1000 genomes]
rs73367500	1.00[ASN][1000 genomes]
rs73368504	1.00[EUR][1000 genomes]
rs73368506	1.00[EUR][1000 genomes]
rs73368523	1.00[EUR][1000 genomes]
rs73380344	1.00[EUR][1000 genomes]
rs8128684	1.00[EUR][1000 genomes]
rs8129300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8129337	1.00[JPT][hapmap]
rs8129839	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8132608	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8132951	1.00[EUR][1000 genomes]
rs8133408	1.00[EUR][1000 genomes]
rs8133774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8134294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8134501	1.00[EUR][1000 genomes]
rs8134648	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9305773	1.00[EUR][1000 genomes]
rs9975878	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[ASN][1000 genomes]
rs9976320	1.00[EUR][1000 genomes]
rs9976683	1.00[EUR][1000 genomes]
rs9977113	0.96[ASN][1000 genomes]
rs9977870	1.00[EUR][1000 genomes]
rs9981475	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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17887000-17906000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:17894200-17906200	Weak transcription	Left Ventricle	heart
3	chr21:17894200-17906800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr21:17898800-17906000	Weak transcription	Psoas Muscle	Psoas
5	chr21:17903600-17906800	Enhancers	HUVEC	blood vessel
6	chr21:17904000-17906600	Weak transcription	Fetal Kidney	kidney
7	chr21:17904200-17906000	Enhancers	Brain Anterior Caudate	brain
8	chr21:17904400-17906000	Enhancers	Brain Cingulate Gyrus	brain
9	chr21:17904400-17907400	Enhancers	Hela-S3	cervix
10	chr21:17904600-17906000	Enhancers	Brain Germinal Matrix	brain
11	chr21:17904600-17906000	Weak transcription	Fetal Muscle Leg	muscle
12	chr21:17904600-17906000	Enhancers	Rectal Smooth Muscle	rectum
13	chr21:17904600-17906200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr21:17904600-17906200	Weak transcription	Esophagus	oesophagus
15	chr21:17904600-17906200	Enhancers	Fetal Lung	lung
16	chr21:17904600-17914200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr21:17905000-17906000	Enhancers	Brain Hippocampus Middle	brain
18	chr21:17905000-17906000	Enhancers	Osteobl	bone
19	chr21:17905000-17906200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr21:17905000-17906200	Enhancers	Fetal Heart	heart
21	chr21:17905200-17906000	Enhancers	Fetal Brain Male	brain
22	chr21:17905200-17906000	Enhancers	HSMMtube	muscle
23	chr21:17905200-17906200	Enhancers	Colon Smooth Muscle	Colon
24	chr21:17905400-17906000	Weak transcription	Brain Angular Gyrus	brain
25	chr21:17905400-17906000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr21:17905400-17906000	Enhancers	NH-A	brain
27	chr21:17905400-17906000	Enhancers	NHDF-Ad	bronchial
28	chr21:17905400-17906400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr21:17905400-17906400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr21:17905400-17906400	Flanking Active TSS	Fetal Brain Female	brain
31	chr21:17905400-17906600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr21:17905400-17906800	Flanking Active TSS	A549	lung
33	chr21:17905400-17907200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr21:17905600-17906000	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr21:17905600-17906000	Weak transcription	Ovary	ovary
36	chr21:17905600-17906000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr21:17905600-17906000	Enhancers	HSMM	muscle
38	chr21:17905600-17906200	Enhancers	NHLF	lung
39	chr21:17905600-17906400	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr21:17905600-17906600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr21:17905600-17906600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr21:17905600-17907800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr21:17905600-17909200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr21:17905800-17906000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr21:17905800-17906000	Flanking Active TSS	Liver	Liver
46	chr21:17905800-17906000	Active TSS	Right Atrium	heart
47	chr21:17905800-17906600	Enhancers	Fetal Stomach	stomach
48	chr21:17905800-17906600	Active TSS	Stomach Smooth Muscle	stomach
49	chr21:17905800-17910200	Active TSS	Brain Substantia Nigra	brain
50	chr21:17905800-17910600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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