Variant report

Variant	rs3803998
Chromosome Location	chr21:17958849-17958850
allele	C/T
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	chr21:17958474-17958850	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr21:17958321-17961589	SK-N-SH	brain:	n/a	n/a
3	MYC	chr21:17958609-17959089	MCF10A-Er-Src	breast:	n/a	n/a
4	BRCA1	chr21:17958735-17961407	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000269950	TF binding region
LINC00478	TF binding region
MIR125B2	TF binding region

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

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

rs_ID	r²[population]
rs17000140	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2000782	1.00[ASN][1000 genomes]
rs2186869	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823882	0.88[GIH][hapmap];1.00[TSI][hapmap]
rs2823887	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2823889	0.83[ASN][1000 genomes]
rs28488116	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58627197	1.00[ASN][1000 genomes]
rs7283757	1.00[ASN][1000 genomes]
rs73363543	1.00[ASN][1000 genomes]
rs73363546	0.92[ASN][1000 genomes]
rs73371307	1.00[ASN][1000 genomes]
rs73371330	1.00[ASN][1000 genomes]
rs8130291	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9980357	0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs9980758	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9982294	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9984854	1.00[ASN][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	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

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17925400-17960400	Weak transcription	Esophagus	oesophagus
2	chr21:17936800-17959400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:17950400-17959000	Weak transcription	Fetal Brain Male	brain
4	chr21:17952000-17959200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr21:17952200-17959000	Weak transcription	NHDF-Ad	bronchial
6	chr21:17952200-17959200	Weak transcription	Aorta	Aorta
7	chr21:17952200-17959400	Weak transcription	Fetal Muscle Leg	muscle
8	chr21:17952200-17959400	Weak transcription	Left Ventricle	heart
9	chr21:17952200-17959400	Weak transcription	Ovary	ovary
10	chr21:17952200-17959400	Weak transcription	NH-A	brain
11	chr21:17953400-17959200	Weak transcription	Brain Angular Gyrus	brain
12	chr21:17953400-17959400	Weak transcription	HSMM	muscle
13	chr21:17953600-17959200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr21:17953600-17959400	Weak transcription	Adipose Nuclei	Adipose
15	chr21:17955800-17959400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr21:17956200-17959200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr21:17957000-17959400	Weak transcription	Pancreas	Pancrea
18	chr21:17957200-17959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr21:17958200-17959000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr21:17958400-17959000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr21:17958400-17959000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr21:17958400-17959200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr21:17958400-17959200	Enhancers	Liver	Liver
24	chr21:17958400-17959200	Enhancers	Brain Germinal Matrix	brain
25	chr21:17958400-17959200	Enhancers	Fetal Lung	lung
26	chr21:17958400-17959200	Enhancers	HUVEC	blood vessel
27	chr21:17958400-17959400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr21:17958400-17959400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr21:17958400-17960200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr21:17958400-17960200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr21:17958600-17959000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr21:17958600-17959000	Enhancers	Brain Substantia Nigra	brain
33	chr21:17958600-17959000	Enhancers	Fetal Brain Female	brain
34	chr21:17958600-17959000	Enhancers	Right Atrium	heart
35	chr21:17958600-17959000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr21:17958600-17959000	Enhancers	Osteobl	bone
37	chr21:17958600-17959200	Enhancers	Brain Anterior Caudate	brain
38	chr21:17958600-17959200	Enhancers	Brain Hippocampus Middle	brain
39	chr21:17958600-17960000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr21:17958600-17960000	Flanking Active TSS	Hela-S3	cervix
41	chr21:17958600-17960400	Enhancers	Fetal Heart	heart
42	chr21:17958800-17959000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr21:17958800-17959000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr21:17958800-17959000	Enhancers	NHEK	skin
45	chr21:17958800-17959200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr21:17958800-17959200	Enhancers	Colon Smooth Muscle	Colon
47	chr21:17958800-17959200	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr21:17958800-17959200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr21:17958800-17959200	Flanking Active TSS	A549	lung
50	chr21:17958800-17959400	Enhancers	HSMMtube	muscle

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