Variant report

Variant	rs17399522
Chromosome Location	chr5:96027637-96027638
allele	C/T
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	CEBPB	chr5:96027179-96027936	Hela-S3	cervix:	n/a	chr5:96027770-96027781 chr5:96027770-96027783
2	PBX3	chr5:96027334-96027776	SK-N-SH	brain:	n/a	n/a
3	MYC	chr5:96027296-96027672	K562	blood:	n/a	n/a
4	CEBPB	chr5:96027181-96027836	HepG2	liver:	n/a	chr5:96027770-96027781 chr5:96027770-96027783
5	MAFK	chr5:96027444-96027796	K562	blood:	n/a	chr5:96027685-96027695
6	MAFF	chr5:96027454-96027734	K562	blood:	n/a	n/a
7	MYC	chr5:96026555-96027653	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr5:96027284-96027953	IMR90	lung:	n/a	chr5:96027770-96027781 chr5:96027770-96027783

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95930369..95932289-chr5:96026143..96027924,2	K562	blood:

Variant related genes	Relation type
CAST	TF binding region
ENSG00000264129	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17086504	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17398838	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17398914	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17399025	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17399215	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17477045	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17477471	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55804164	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56214211	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73774355	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95999400-96038000	Weak transcription	Fetal Stomach	stomach
2	chr5:95999600-96028200	Weak transcription	Aorta	Aorta
3	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung
5	chr5:96000800-96037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:96001600-96037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:96002400-96027800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:96002400-96037600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:96002400-96038200	Weak transcription	Esophagus	oesophagus
10	chr5:96004800-96028200	Weak transcription	Lung	lung
11	chr5:96004800-96036600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:96005000-96038000	Weak transcription	Ovary	ovary
13	chr5:96005000-96038200	Weak transcription	Gastric	stomach
14	chr5:96005600-96027800	Weak transcription	Left Ventricle	heart
15	chr5:96007600-96027800	Weak transcription	Fetal Intestine Large	intestine
16	chr5:96009200-96037600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:96013000-96037800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:96013600-96031400	Weak transcription	Stomach Mucosa	stomach
19	chr5:96013800-96037600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:96014000-96030800	Weak transcription	HSMM	muscle
21	chr5:96015400-96031800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:96016200-96031600	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:96016600-96035200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr5:96016800-96027800	Weak transcription	Right Atrium	heart
25	chr5:96016800-96035000	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:96016800-96038200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:96017000-96034000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:96017000-96038000	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:96018800-96038200	Weak transcription	Colonic Mucosa	Colon
30	chr5:96018800-96038200	Weak transcription	Spleen	Spleen
31	chr5:96019000-96031600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:96019400-96031600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr5:96021800-96027800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:96021800-96032000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:96022200-96031600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr5:96022200-96034800	Weak transcription	NH-A	brain
37	chr5:96022400-96031600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:96023000-96027800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:96023000-96030400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr5:96023000-96035000	Weak transcription	Right Ventricle	heart
41	chr5:96023000-96038400	Weak transcription	Small Intestine	intestine
42	chr5:96023200-96037600	Weak transcription	Thymus	Thymus
43	chr5:96023400-96031200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:96023400-96032000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr5:96023600-96031200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:96023600-96033000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:96023600-96035000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:96023600-96036800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:96023800-96027800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:96023800-96028200	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links