Variant report

Variant	rs2823898
Chromosome Location	chr21:17965220-17965221
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17960195..17962509-chr21:17965185..17966812,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215386	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2018708	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2823897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823899	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2823900	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823903	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2823904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823905	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2823906	1.00[CEU][hapmap]
rs2823907	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2823908	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28547508	0.85[EUR][1000 genomes]
rs915763	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs915764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9284478	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9305771	0.85[EUR][1000 genomes]
rs9305772	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9976817	0.85[EUR][1000 genomes]
rs9978710	0.85[EUR][1000 genomes]
rs9980971	0.85[EUR][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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17960000-17970600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr21:17961200-17968400	Weak transcription	Liver	Liver
3	chr21:17961200-17970200	Weak transcription	Psoas Muscle	Psoas
4	chr21:17961200-17971200	Weak transcription	Esophagus	oesophagus
5	chr21:17961200-17978000	Weak transcription	Fetal Muscle Leg	muscle
6	chr21:17961200-17978000	Weak transcription	Left Ventricle	heart
7	chr21:17961200-17978000	Weak transcription	Ovary	ovary
8	chr21:17961200-17979200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr21:17961200-17985200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr21:17961200-18003800	Weak transcription	Aorta	Aorta
11	chr21:17961400-17968600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr21:17961400-17968800	Weak transcription	Fetal Kidney	kidney
13	chr21:17961400-17977600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr21:17961400-17983200	Weak transcription	HSMMtube	muscle
15	chr21:17961400-17984000	Weak transcription	Osteobl	bone
16	chr21:17961800-17973400	Weak transcription	HUVEC	blood vessel
17	chr21:17962200-17987800	Weak transcription	Hela-S3	cervix
18	chr21:17963200-17977800	Weak transcription	Adipose Nuclei	Adipose
19	chr21:17963400-17968600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr21:17963400-17977200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr21:17963600-17981400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr21:17964200-17965600	Enhancers	Fetal Lung	lung
23	chr21:17964400-17965800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr21:17964400-17967800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr21:17964600-17965400	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr21:17964600-17965600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:17964600-17965600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr21:17964600-17965800	Enhancers	Brain Cingulate Gyrus	brain
29	chr21:17964600-17965800	Enhancers	Brain Substantia Nigra	brain
30	chr21:17964800-17965600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr21:17965000-17965400	Enhancers	Brain Hippocampus Middle	brain
32	chr21:17965000-17977600	Weak transcription	Brain Anterior Caudate	brain
33	chr21:17965200-17965600	Weak transcription	Fetal Brain Male	brain
34	chr21:17965200-17965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr21:17965200-17966600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr21:17965200-17970000	Weak transcription	Fetal Brain Female	brain
37	chr21:17965200-17977200	Weak transcription	Brain Angular Gyrus	brain

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