Variant report

Variant	rs7277885
Chromosome Location	chr21:17959166-17959167
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	MXI1	chr21:17958321-17961589	SK-N-SH	brain:	n/a	n/a
2	EP300	chr21:17959013-17961175	Hela-S3	cervix:	n/a	chr21:17960142-17960151 chr21:17959459-17959469 chr21:17959359-17959373 chr21:17959874-17959883 chr21:17960737-17960751 chr21:17960881-17960897 chr21:17960649-17960663 chr21:17959870-17959884 chr21:17960730-17960744
3	POLR2A	chr21:17959137-17959968	U87	brain:	n/a	n/a
4	RCOR1	chr21:17958900-17961090	Hela-S3	cervix:	n/a	n/a
5	BRCA1	chr21:17958735-17961407	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17924356..17926618-chr21:17958944..17960666,2	MCF-7	breast:

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

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2823824	1.00[MEX][hapmap]
rs2823857	1.00[MEX][hapmap]
rs58268745	1.00[EUR][1000 genomes]
rs7278514	1.00[EUR][1000 genomes]
rs73371344	1.00[EUR][1000 genomes]
rs73371348	1.00[EUR][1000 genomes]
rs762301	1.00[EUR][1000 genomes]
rs8128702	1.00[EUR][1000 genomes]
rs9284477	1.00[EUR][1000 genomes]
rs9305770	1.00[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:57 , 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	chr21:17952000-17959200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:17952200-17959200	Weak transcription	Aorta	Aorta
5	chr21:17952200-17959400	Weak transcription	Fetal Muscle Leg	muscle
6	chr21:17952200-17959400	Weak transcription	Left Ventricle	heart
7	chr21:17952200-17959400	Weak transcription	Ovary	ovary
8	chr21:17952200-17959400	Weak transcription	NH-A	brain
9	chr21:17953400-17959200	Weak transcription	Brain Angular Gyrus	brain
10	chr21:17953400-17959400	Weak transcription	HSMM	muscle
11	chr21:17953600-17959200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr21:17953600-17959400	Weak transcription	Adipose Nuclei	Adipose
13	chr21:17955800-17959400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr21:17956200-17959200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr21:17957000-17959400	Weak transcription	Pancreas	Pancrea
16	chr21:17958400-17959200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr21:17958400-17959200	Enhancers	Liver	Liver
18	chr21:17958400-17959200	Enhancers	Brain Germinal Matrix	brain
19	chr21:17958400-17959200	Enhancers	Fetal Lung	lung
20	chr21:17958400-17959200	Enhancers	HUVEC	blood vessel
21	chr21:17958400-17959400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr21:17958400-17959400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr21:17958400-17960200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr21:17958400-17960200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr21:17958600-17959200	Enhancers	Brain Anterior Caudate	brain
26	chr21:17958600-17959200	Enhancers	Brain Hippocampus Middle	brain
27	chr21:17958600-17960000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr21:17958600-17960000	Flanking Active TSS	Hela-S3	cervix
29	chr21:17958600-17960400	Enhancers	Fetal Heart	heart
30	chr21:17958800-17959200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr21:17958800-17959200	Enhancers	Colon Smooth Muscle	Colon
32	chr21:17958800-17959200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr21:17958800-17959200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr21:17958800-17959200	Flanking Active TSS	A549	lung
35	chr21:17958800-17959400	Enhancers	HSMMtube	muscle
36	chr21:17958800-17959800	Flanking Active TSS	HMEC	breast
37	chr21:17958800-17960200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr21:17958800-17961200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr21:17959000-17959200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr21:17959000-17959200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr21:17959000-17959200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr21:17959000-17959200	Active TSS	Brain Substantia Nigra	brain
43	chr21:17959000-17959200	Enhancers	Fetal Brain Male	brain
44	chr21:17959000-17959400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr21:17959000-17959400	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr21:17959000-17959400	Enhancers	NHDF-Ad	bronchial
47	chr21:17959000-17959400	Active TSS	NHLF	lung
48	chr21:17959000-17959600	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr21:17959000-17960000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr21:17959000-17960000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links