Variant report

Variant	rs56930352
Chromosome Location	chr21:17790937-17790938
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	KAP1	chr21:17790827-17793051	HEK293	kidney:	n/a	chr21:17792628-17792636
2	MXI1	chr21:17790501-17793068	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LINC00478	TF binding region

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1974156	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1974158	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2823789	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2823794	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2823806	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73357766	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73357775	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73357787	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8129788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs996177	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9974511	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv913416	chr21:17728224-17863882	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv913419	chr21:17775056-17826260	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv470880	chr21:17777827-17820111	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv459100	chr21:17777966-17826260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv587077	chr21:17777966-17826260	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv913420	chr21:17777966-17826260	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv913421	chr21:17786219-17826260	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17771400-17791200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr21:17788800-17791000	Weak transcription	Ovary	ovary
3	chr21:17789400-17791200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr21:17789600-17791000	Enhancers	Fetal Brain Male	brain
5	chr21:17789600-17791400	Enhancers	Brain Hippocampus Middle	brain
6	chr21:17790000-17791400	Enhancers	Brain Substantia Nigra	brain
7	chr21:17790200-17791400	Enhancers	Liver	Liver
8	chr21:17790400-17791000	Enhancers	Brain Germinal Matrix	brain
9	chr21:17790400-17791400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr21:17790400-17791400	Enhancers	HUVEC	blood vessel
11	chr21:17790400-17791600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr21:17790400-17792400	Flanking Active TSS	Osteobl	bone
13	chr21:17790400-17793000	Active TSS	Psoas Muscle	Psoas
14	chr21:17790400-17797000	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr21:17790600-17791000	Active TSS	Aorta	Aorta
16	chr21:17790600-17791000	Active TSS	Brain Angular Gyrus	brain
17	chr21:17790600-17791000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr21:17790600-17791200	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr21:17790600-17791200	Enhancers	A549	lung
20	chr21:17790600-17791400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr21:17790600-17791400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr21:17790600-17793000	Active TSS	Right Ventricle	heart
23	chr21:17790600-17793200	Active TSS	Right Atrium	heart
24	chr21:17790800-17791000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr21:17790800-17791000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr21:17790800-17791000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr21:17790800-17791000	Flanking Active TSS	Fetal Heart	heart
28	chr21:17790800-17791000	Enhancers	Stomach Smooth Muscle	stomach
29	chr21:17790800-17791000	Enhancers	Hela-S3	cervix
30	chr21:17790800-17791000	Enhancers	HSMM	muscle
31	chr21:17790800-17791200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr21:17790800-17791200	Flanking Active TSS	Fetal Brain Female	brain
33	chr21:17790800-17791400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr21:17790800-17791400	Enhancers	Brain Cingulate Gyrus	brain
35	chr21:17790800-17791400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr21:17790800-17791400	Enhancers	Fetal Lung	lung
37	chr21:17790800-17791400	Enhancers	Rectal Smooth Muscle	rectum
38	chr21:17790800-17791400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr21:17790800-17791400	Enhancers	NH-A	brain
40	chr21:17790800-17791600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr21:17790800-17791600	Enhancers	Colon Smooth Muscle	Colon
42	chr21:17790800-17791600	Flanking Active TSS	HSMMtube	muscle
43	chr21:17790800-17791800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr21:17790800-17793000	Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links