Variant report

Variant	rs41280320
Chromosome Location	chr20:1357933-1357934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:1357816-1358473	GM12892	blood:	n/a	n/a
2	POLR2A	chr20:1356277-1358121	GM12878	blood:	n/a	n/a
3	POLR2A	chr20:1357528-1361515	PANC-1	pancreas:	n/a	n/a
4	IRF4	chr20:1357878-1358362	GM12878	blood:	n/a	n/a
5	RELA	chr20:1357040-1358365	GM12878	blood:	n/a	n/a
6	EBF1	chr20:1357871-1358694	GM12878	blood:	n/a	n/a
7	POLR2A	chr20:1357766-1358408	GM12892	blood:	n/a	n/a
8	RUNX3	chr20:1357789-1358655	GM12878	blood:	n/a	n/a
9	MTA3	chr20:1357363-1358634	GM12878	blood:	n/a	n/a
10	NFIC	chr20:1357875-1358670	GM12878	blood:	n/a	n/a
11	BATF	chr20:1357930-1358395	GM12878	blood:	n/a	chr20:1358164-1358175
12	POLR2A	chr20:1357856-1358466	GM12892	blood:	n/a	n/a
13	RELA	chr20:1356783-1358122	GM19099	blood:	n/a	n/a
14	CHD2	chr20:1357441-1358350	GM12878	blood:	n/a	n/a
15	EP300	chr20:1357483-1358376	GM12878	blood:	n/a	n/a
16	RELA	chr20:1356304-1358402	GM12891	blood:	n/a	n/a
17	SPI1	chr20:1357102-1358330	GM12878	blood:	n/a	n/a
18	MAZ	chr20:1357594-1358087	GM12878	blood:	n/a	n/a
19	POU2F2	chr20:1357918-1358294	GM12891	blood:	n/a	n/a
20	STAT3	chr20:1357810-1358010	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr20:1357805-1358364	GM12878	blood:	n/a	n/a
22	MXI1	chr20:1357424-1358447	GM12878	blood:	n/a	n/a
23	ATF2	chr20:1357905-1358424	GM12878	blood:	n/a	n/a
24	POLR2A	chr20:1357850-1358555	GM12891	blood:	n/a	n/a
25	POLR2A	chr20:1357367-1357976	PFSK-1	brain:	n/a	n/a
26	RUNX3	chr20:1357776-1358644	GM12878	blood:	n/a	n/a
27	POLR2A	chr20:1355853-1361695	HUVEC	blood vessel:	n/a	n/a
28	NFATC1	chr20:1357900-1358394	GM12878	blood:	n/a	n/a
29	POLR2A	chr20:1357918-1358529	GM12892	blood:	n/a	n/a
30	CUX1	chr20:1357430-1357939	GM12878	blood:	n/a	n/a
31	EBF1	chr20:1356427-1358958	GM12878	blood:	n/a	n/a
32	CHD1	chr20:1357134-1358231	GM12878	blood:	n/a	n/a
33	POLR2A	chr20:1357829-1358452	GM12891	blood:	n/a	n/a
34	IKZF1	chr20:1357092-1358710	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:1351705..1353589-chr20:1357779..1360350,3	K562	blood:
2	chr20:1352089..1353589-chr20:1357859..1360350,2	K562	blood:
3	chr20:1356708..1360006-chr20:1370558..1373951,3	K562	blood:
4	chr20:1307748..1310698-chr20:1356609..1358929,2	K562	blood:

No data

Variant related genes	Relation type
FKBP1A	TF binding region
ENSG00000088832	Chromatin interaction
ENSG00000125775	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs4814111	1.00[ASN][1000 genomes]
rs73067243	1.00[ASN][1000 genomes]
rs73081763	1.00[ASN][1000 genomes]
rs73083845	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1327600-1372200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:1331600-1358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr20:1336200-1361800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr20:1336400-1370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:1341400-1370600	Weak transcription	Hela-S3	cervix
6	chr20:1345600-1358000	Weak transcription	Stomach Mucosa	stomach
7	chr20:1347600-1359000	Strong transcription	Fetal Stomach	stomach
8	chr20:1348000-1366800	Strong transcription	Dnd41	blood
9	chr20:1349000-1362800	Weak transcription	Fetal Kidney	kidney
10	chr20:1351000-1359200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr20:1351800-1358200	Weak transcription	Aorta	Aorta
12	chr20:1353200-1358000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr20:1353200-1369400	Weak transcription	Brain Germinal Matrix	brain
14	chr20:1353800-1358400	Genic enhancers	Primary T cells from cord blood	blood
15	chr20:1354200-1360600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:1354400-1358000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:1354400-1358200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr20:1354400-1371200	Weak transcription	Fetal Brain Male	brain
19	chr20:1354600-1358000	Weak transcription	Gastric	stomach
20	chr20:1354600-1358000	Weak transcription	Ovary	ovary
21	chr20:1354600-1358200	Weak transcription	Esophagus	oesophagus
22	chr20:1354600-1363400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr20:1355200-1359800	Enhancers	Psoas Muscle	Psoas
24	chr20:1355400-1358600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr20:1355400-1358800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr20:1355400-1369000	Weak transcription	Fetal Brain Female	brain
27	chr20:1355600-1358000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr20:1355600-1362800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr20:1355600-1366400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr20:1355600-1369600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr20:1355800-1359000	Enhancers	NHDF-Ad	bronchial
32	chr20:1356000-1358000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr20:1356000-1358200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr20:1356000-1358200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr20:1356000-1358600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr20:1356000-1358800	Enhancers	Primary hematopoietic stem cells	blood
37	chr20:1356000-1359000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr20:1356000-1360200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr20:1356000-1361000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr20:1356000-1362400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr20:1356200-1358600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr20:1356200-1358800	Enhancers	Spleen	Spleen
43	chr20:1356200-1359000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr20:1356200-1359200	Enhancers	Osteobl	bone
45	chr20:1356200-1360600	Genic enhancers	Rectal Mucosa Donor 29	rectum
46	chr20:1356200-1361000	Enhancers	Duodenum Mucosa	Duodenum
47	chr20:1356200-1361200	Enhancers	Brain Cingulate Gyrus	brain
48	chr20:1356200-1363000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr20:1356400-1358000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr20:1356400-1358200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links