Variant report

Variant	rs213888
Chromosome Location	chr5:94981993-94981994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr5:94981989-94983295	SH-SY5Y	brain:	n/a	n/a
2	NR2F2	chr5:94981919-94982886	MCF-7	breast:	n/a	n/a
3	POLR2A	chr5:94981971-94983108	K562	blood:	n/a	n/a
4	SMARCB1	chr5:94981977-94983148	Hela-S3	cervix:	n/a	n/a
5	CBX3	chr5:94981910-94983105	K562	blood:	n/a	n/a
6	SIN3AK20	chr5:94981901-94983194	MCF-7	breast:	n/a	n/a
7	GATA3	chr5:94981976-94982797	MCF-7	breast:	n/a	n/a
8	HA-E2F1	chr5:94981844-94983270	MCF-7	breast:	n/a	chr5:94982435-94982444 chr5:94982545-94982554 chr5:94982226-94982235 chr5:94982399-94982408
9	GATA3	chr5:94981951-94982906	SK-N-SH	brain:	n/a	n/a
10	SETDB1	chr5:94981808-94983052	U2OS	brain:	n/a	n/a
11	NFYB	chr5:94981793-94982647	K562	blood:	n/a	n/a
12	MXI1	chr5:94981967-94983773	SK-N-SH	brain:	n/a	chr5:94982918-94982927 chr5:94982416-94982425
13	GATA3	chr5:94981957-94982617	T-47D	breast:	n/a	n/a
14	GATA3	chr5:94981955-94982780	T-47D	breast:	n/a	n/a
15	GATA3	chr5:94981895-94982824	MCF-7	breast:	n/a	n/a
16	GATA3	chr5:94981983-94982720	MCF-7	breast:	n/a	n/a
17	GATA1	chr5:94981455-94985033	PBDE	blood:	n/a	chr5:94984644-94984654 chr5:94983869-94983879 chr5:94984445-94984453 chr5:94984371-94984388 chr5:94983800-94983811 chr5:94983693-94983709
18	SIN3AK20	chr5:94981821-94983195	MCF-7	breast:	n/a	n/a
19	GATA3	chr5:94981957-94982852	SK-N-SH	brain:	n/a	n/a
20	TCF12	chr5:94981954-94983497	A549	lung:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:94979518..94982436-chr5:95080869..95082973,2	K562	blood:
2	chr5:94981556..94984192-chr5:95101303..95104225,2	MCF-7	breast:
3	chr5:94981368..94988467-chr5:95046173..95051252,17	K562	blood:
4	chr5:94977116..95012475-chr5:95055682..95079552,215	K562	blood:
5	chr5:94980512..95018354-chr5:95057997..95080764,228	K562	blood:
6	chr5:94979988..94984168-chr5:95032454..95035928,4	MCF-7	breast:
7	chr5:94888891..94893786-chr5:94981389..94987516,11	K562	blood:
8	chr5:94980020..94983633-chr5:95104411..95107623,3	K562	blood:
9	chr5:94980861..94985410-chr5:95067178..95071099,5	MCF-7	breast:
10	chr5:94889492..94895025-chr5:94981557..94985063,8	K562	blood:
11	chr5:90676216..90679010-chr5:94981409..94984145,2	K562	blood:
12	chr5:94979766..94982277-chr5:95116115..95117894,2	MCF-7	breast:
13	chr5:94979878..94983810-chr5:95295717..95298674,4	K562	blood:
14	chr5:94979432..94984462-chr5:95062276..95069972,15	MCF-7	breast:
15	chr5:94981340..94984731-chr5:95103817..95108133,4	K562	blood:
16	chr5:94953878..94956024-chr5:94981084..94983825,2	K562	blood:
17	chr5:94981287..94984175-chr5:95296229..95298674,3	K562	blood:
18	chr5:94981172..94985318-chr5:95169805..95176246,5	MCF-7	breast:

No data

Variant related genes	Relation type
RFESD	TF binding region
ENSG00000251000	Chromatin interaction
ENSG00000118985	Chromatin interaction
ENSG00000164291	Chromatin interaction
ENSG00000251314	Chromatin interaction
ENSG00000164292	Chromatin interaction
ENSG00000178015	Chromatin interaction
ENSG00000250240	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000145757	Chromatin interaction
ENSG00000251348	Chromatin interaction
ENSG00000198677	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10063774	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13166682	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13172592	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13179768	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs150548	0.94[ASN][1000 genomes]
rs150549	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs150550	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213507	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213508	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213509	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213510	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213511	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213512	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213880	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213885	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213887	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411817	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412026	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs440342	0.99[ASN][1000 genomes]
rs4869245	0.95[ASN][1000 genomes]
rs6865873	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6890832	0.80[EUR][1000 genomes];0.99[ASN][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	nsv598955	chr5:94903453-95136019	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv598960	chr5:94975592-94988482	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94976000-94982400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:94976800-94982200	Enhancers	Liver	Liver
3	chr5:94977600-94982200	Weak transcription	Right Atrium	heart
4	chr5:94977600-94982200	Weak transcription	HSMM	muscle
5	chr5:94977800-94982000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:94977800-94982000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:94977800-94982600	Weak transcription	Left Ventricle	heart
8	chr5:94978000-94982200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:94978000-94982600	Weak transcription	Aorta	Aorta
10	chr5:94979200-94982200	Weak transcription	Pancreas	Pancrea
11	chr5:94979800-94982000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr5:94979800-94982200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:94980000-94982600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:94980200-94982000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:94980200-94982000	Enhancers	HepG2	liver
16	chr5:94980200-94982200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:94980200-94982200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:94980200-94982200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:94980200-94982200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:94980200-94982200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr5:94980200-94982200	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:94980200-94982200	Weak transcription	NHDF-Ad	bronchial
23	chr5:94980200-94982200	Weak transcription	NHEK	skin
24	chr5:94980200-94982200	Weak transcription	NHLF	lung
25	chr5:94980400-94982000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr5:94980400-94982000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr5:94980400-94982200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr5:94980400-94982200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:94980400-94982200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:94980400-94982200	Weak transcription	Fetal Thymus	thymus
31	chr5:94980400-94982200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:94980400-94982200	Weak transcription	GM12878-XiMat	blood
33	chr5:94980400-94982200	Weak transcription	Osteobl	bone
34	chr5:94980600-94982000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:94980600-94982000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:94980600-94982200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:94980600-94982200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:94980600-94982200	Weak transcription	Brain Substantia Nigra	brain
39	chr5:94980600-94982200	Weak transcription	Stomach Mucosa	stomach
40	chr5:94980600-94982200	Weak transcription	K562	blood
41	chr5:94980600-94982600	Weak transcription	Colon Smooth Muscle	Colon
42	chr5:94980800-94982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:94981200-94982000	Weak transcription	Hela-S3	cervix
44	chr5:94981200-94982200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:94981200-94982200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:94981400-94982000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr5:94981400-94982200	Weak transcription	Primary T cells from cord blood	blood
48	chr5:94981600-94982000	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr5:94981600-94982000	Enhancers	Dnd41	blood
50	chr5:94981600-94982400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links