Variant report

Variant	rs55954827
Chromosome Location	chr21:17442997-17442998
allele	A/C
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	MYC	chr21:17442993-17443082	MCF10A-Er-Src	breast:	n/a	n/a
2	TAF1	chr21:17442540-17443077	PFSK-1	brain:	n/a	n/a
3	GATA2	chr21:17442412-17443768	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr21:17442331-17444053	PFSK-1	brain:	n/a	n/a
5	MXI1	chr21:17441476-17443970	SK-N-SH	brain:	n/a	n/a
6	EP300	chr21:17441902-17444931	SK-N-SH	brain:	n/a	chr21:17442640-17442654 chr21:17443209-17443219 chr21:17442634-17442642 chr21:17442984-17442998
7	POLR2A	chr21:17442391-17443194	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr21:17442543-17443083	U87	brain:	n/a	n/a
9	POLR2A	chr21:17442684-17443057	U87	brain:	n/a	n/a

Variant related genes	Relation type
LINC00478	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs59305213	1.00[AFR][1000 genomes]
rs73894712	1.00[AFR][1000 genomes]
rs73894740	1.00[AFR][1000 genomes]
rs73894742	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913414	chr21:17383785-17459507	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv913415	chr21:17400916-17452276	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2830060	chr21:17400916-17459507	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv527854	chr21:17400916-17459507	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1851038	chr21:17412144-17488119	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17441400-17444000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr21:17441600-17445000	Active TSS	Brain Germinal Matrix	brain
3	chr21:17441600-17446800	Active TSS	Fetal Brain Female	brain
4	chr21:17441800-17443200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr21:17441800-17445400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:17442000-17446200	Active TSS	Brain Angular Gyrus	brain
7	chr21:17442000-17446400	Active TSS	Brain Cingulate Gyrus	brain
8	chr21:17442000-17446800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr21:17442000-17447200	Active TSS	Fetal Brain Male	brain
10	chr21:17442000-17448000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr21:17442400-17443000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr21:17442400-17443000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr21:17442400-17443600	Flanking Active TSS	Osteobl	bone
14	chr21:17442400-17443800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr21:17442400-17443800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr21:17442400-17446200	Active TSS	Brain Anterior Caudate	brain
17	chr21:17442400-17446200	Active TSS	Brain Substantia Nigra	brain
18	chr21:17442600-17443000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr21:17442600-17443000	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr21:17442600-17443000	Enhancers	Fetal Stomach	stomach
21	chr21:17442600-17443000	Active TSS	Rectal Smooth Muscle	rectum
22	chr21:17442600-17443000	Flanking Active TSS	NH-A	brain
23	chr21:17442600-17443200	Enhancers	Fetal Lung	lung
24	chr21:17442600-17443400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr21:17442600-17443400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr21:17442600-17443400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr21:17442600-17443400	Active TSS	Adipose Nuclei	Adipose
28	chr21:17442600-17443400	Active TSS	Fetal Muscle Trunk	muscle
29	chr21:17442600-17443400	Enhancers	NHLF	lung
30	chr21:17442600-17443600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr21:17442600-17443800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr21:17442600-17444000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr21:17442600-17444200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr21:17442600-17444200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr21:17442600-17444200	Active TSS	NHDF-Ad	bronchial
36	chr21:17442600-17444400	Active TSS	Ovary	ovary
37	chr21:17442600-17444600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr21:17442800-17443000	Enhancers	Colon Smooth Muscle	Colon
39	chr21:17442800-17443000	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr21:17442800-17443200	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr21:17442800-17443400	Weak transcription	Fetal Kidney	kidney
42	chr21:17442800-17443600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr21:17442800-17444000	Active TSS	Cortex derived primary cultured neurospheres	brain

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