Variant report

Variant	rs6041827
Chromosome Location	chr20:1358272-1358273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 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	chr20:1358159-1358364	HUVEC	blood vessel:	n/a	n/a
3	WRNIP1	chr20:1358048-1358712	GM12878	blood:	n/a	n/a
4	POLR2A	chr20:1357528-1361515	PANC-1	pancreas:	n/a	n/a
5	IRF4	chr20:1357878-1358362	GM12878	blood:	n/a	n/a
6	RELA	chr20:1357040-1358365	GM12878	blood:	n/a	n/a
7	EBF1	chr20:1357871-1358694	GM12878	blood:	n/a	n/a
8	POLR2A	chr20:1357766-1358408	GM12892	blood:	n/a	n/a
9	STAT3	chr20:1358002-1358281	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr20:1358063-1358917	HepG2	liver:	n/a	n/a
11	MAX	chr20:1358233-1358293	GM12878	blood:	n/a	n/a
12	BATF	chr20:1357980-1358388	GM12878	blood:	n/a	chr20:1358164-1358175
13	RFX5	chr20:1358134-1358425	GM12878	blood:	n/a	n/a
14	STAT3	chr20:1358099-1358356	GM12878	blood:	n/a	n/a
15	RUNX3	chr20:1357789-1358655	GM12878	blood:	n/a	n/a
16	MTA3	chr20:1357363-1358634	GM12878	blood:	n/a	n/a
17	NFIC	chr20:1357875-1358670	GM12878	blood:	n/a	n/a
18	BATF	chr20:1357930-1358395	GM12878	blood:	n/a	chr20:1358164-1358175
19	POLR2A	chr20:1357856-1358466	GM12892	blood:	n/a	n/a
20	CHD2	chr20:1357441-1358350	GM12878	blood:	n/a	n/a
21	EP300	chr20:1357483-1358376	GM12878	blood:	n/a	n/a
22	RELA	chr20:1356304-1358402	GM12891	blood:	n/a	n/a
23	POLR2A	chr20:1358272-1359038	K562	blood:	n/a	n/a
24	TBP	chr20:1357994-1358291	GM12878	blood:	n/a	n/a
25	SPI1	chr20:1357102-1358330	GM12878	blood:	n/a	n/a
26	POU2F2	chr20:1357918-1358294	GM12891	blood:	n/a	n/a
27	ZNF143	chr20:1358109-1358309	GM12878	blood:	n/a	n/a
28	POLR2A	chr20:1357805-1358364	GM12878	blood:	n/a	n/a
29	MXI1	chr20:1357424-1358447	GM12878	blood:	n/a	n/a
30	ATF2	chr20:1357905-1358424	GM12878	blood:	n/a	n/a
31	POLR2A	chr20:1357850-1358555	GM12891	blood:	n/a	n/a
32	RUNX3	chr20:1357776-1358644	GM12878	blood:	n/a	n/a
33	POLR2A	chr20:1355853-1361695	HUVEC	blood vessel:	n/a	n/a
34	NFATC1	chr20:1357900-1358394	GM12878	blood:	n/a	n/a
35	POLR2A	chr20:1357918-1358529	GM12892	blood:	n/a	n/a
36	EBF1	chr20:1356427-1358958	GM12878	blood:	n/a	n/a
37	POLR2A	chr20:1357829-1358452	GM12891	blood:	n/a	n/a
38	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: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1998006	1.00[MEX][hapmap]
rs41280324	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4505594	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56295224	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6033554	0.82[ASW][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap]
rs6033572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6033581	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6041716	0.91[YRI][hapmap]
rs6041734	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap]
rs6041759	1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6041772	1.00[CEU][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6041774	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6041846	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6041861	0.94[LWK][hapmap]
rs6041891	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6041892	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60669872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62186862	0.96[EUR][1000 genomes]
rs62187549	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6514337	0.95[YRI][hapmap]
rs6514339	0.82[CEU][hapmap]
rs7274574	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73079666	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73079672	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8117563	0.86[YRI][hapmap]

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	chr20:1336200-1361800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:1336400-1370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:1341400-1370600	Weak transcription	Hela-S3	cervix
5	chr20:1347600-1359000	Strong transcription	Fetal Stomach	stomach
6	chr20:1348000-1366800	Strong transcription	Dnd41	blood
7	chr20:1349000-1362800	Weak transcription	Fetal Kidney	kidney
8	chr20:1351000-1359200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr20:1353200-1369400	Weak transcription	Brain Germinal Matrix	brain
10	chr20:1353800-1358400	Genic enhancers	Primary T cells from cord blood	blood
11	chr20:1354200-1360600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr20:1354400-1371200	Weak transcription	Fetal Brain Male	brain
13	chr20:1354600-1363400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr20:1355200-1359800	Enhancers	Psoas Muscle	Psoas
15	chr20:1355400-1358600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr20:1355400-1358800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr20:1355400-1369000	Weak transcription	Fetal Brain Female	brain
18	chr20:1355600-1362800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr20:1355600-1366400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr20:1355600-1369600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr20:1355800-1359000	Enhancers	NHDF-Ad	bronchial
22	chr20:1356000-1358600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr20:1356000-1358800	Enhancers	Primary hematopoietic stem cells	blood
24	chr20:1356000-1359000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr20:1356000-1360200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr20:1356000-1361000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr20:1356000-1362400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr20:1356200-1358600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr20:1356200-1358800	Enhancers	Spleen	Spleen
30	chr20:1356200-1359000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr20:1356200-1359200	Enhancers	Osteobl	bone
32	chr20:1356200-1360600	Genic enhancers	Rectal Mucosa Donor 29	rectum
33	chr20:1356200-1361000	Enhancers	Duodenum Mucosa	Duodenum
34	chr20:1356200-1361200	Enhancers	Brain Cingulate Gyrus	brain
35	chr20:1356200-1363000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr20:1356400-1359000	Enhancers	Primary T cells fromperipheralblood	blood
37	chr20:1356400-1361200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr20:1356400-1361600	Enhancers	Brain Anterior Caudate	brain
39	chr20:1356400-1365600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr20:1356400-1369600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr20:1356600-1358600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr20:1356600-1360000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr20:1356600-1369800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr20:1356800-1358400	Enhancers	Fetal Muscle Leg	muscle
45	chr20:1356800-1359400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr20:1356800-1360200	Enhancers	Primary B cells from peripheral blood	blood
47	chr20:1356800-1361200	Enhancers	Left Ventricle	heart
48	chr20:1356800-1365400	Weak transcription	Colonic Mucosa	Colon
49	chr20:1356800-1369200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr20:1356800-1371800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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