Variant report

Variant	rs2279459
Chromosome Location	chr8:59508433-59508434
allele	C/G
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	EP300	chr8:59508338-59508895	SK-N-SH_RA	brain:	n/a	chr8:59508596-59508610 chr8:59508646-59508660 chr8:59508508-59508517
2	POLR2A	chr8:59508335-59508932	HUVEC	blood vessel:	n/a	n/a
3	RUNX3	chr8:59508416-59508890	GM12878	blood:	n/a	n/a
4	FOS	chr8:59508333-59508901	MCF10A-Er-Src	breast:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
5	EP300	chr8:59508211-59509008	K562	blood:	n/a	chr8:59508596-59508610 chr8:59508646-59508660 chr8:59508508-59508517
6	PBX3	chr8:59507713-59509008	SK-N-SH	brain:	n/a	n/a
7	CEBPB	chr8:59508370-59508859	K562	blood:	n/a	chr8:59508455-59508467
8	PBX3	chr8:59508319-59509046	SK-N-SH	brain:	n/a	n/a
9	RUNX3	chr8:59508302-59508949	GM12878	blood:	n/a	n/a
10	MAX	chr8:59508419-59508941	NB4	blood:	n/a	chr8:59508508-59508517 chr8:59508694-59508703
11	MXI1	chr8:59508352-59509054	GM12878	blood:	n/a	n/a
12	POLR2A	chr8:59508399-59508986	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr8:59508417-59508840	K562	blood:	n/a	chr8:59508455-59508467
14	GATA1	chr8:59508292-59509100	PBDE	blood:	n/a	chr8:59508507-59508516
15	ATF2	chr8:59508421-59508880	GM12878	blood:	n/a	n/a
16	TCF12	chr8:59507804-59509028	SK-N-SH	brain:	n/a	n/a
17	ATF1	chr8:59508388-59508886	K562	blood:	n/a	n/a
18	CEBPB	chr8:59508367-59508858	K562	blood:	n/a	chr8:59508455-59508467
19	NFIC	chr8:59507700-59509006	GM12878	blood:	n/a	n/a
20	JUN	chr8:59508334-59508930	K562	blood:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
21	TEAD4	chr8:59508339-59508967	SK-N-SH	brain:	n/a	n/a
22	BHLHE40	chr8:59508363-59508996	GM12878	blood:	n/a	n/a
23	POLR2A	chr8:59508328-59509078	GM12878	blood:	n/a	n/a
24	POLR2A	chr8:59508370-59509120	U87	brain:	n/a	n/a
25	TCF12	chr8:59507691-59509078	SK-N-SH	brain:	n/a	n/a
26	BATF	chr8:59508431-59508842	GM12878	blood:	n/a	n/a
27	MAX	chr8:59508398-59509041	SK-N-SH	brain:	n/a	chr8:59508508-59508517 chr8:59508694-59508703
28	FOS	chr8:59508003-59508935	HUVEC	blood vessel:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508021-59508033 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
29	POLR2A	chr8:59508318-59508984	U87	brain:	n/a	n/a
30	CEBPB	chr8:59508392-59508844	Hela-S3	cervix:	n/a	chr8:59508455-59508467
31	FOXM1	chr8:59508309-59508946	GM12878	blood:	n/a	n/a
32	JUND	chr8:59508021-59509007	K562	blood:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508021-59508033 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
33	MAX	chr8:59508375-59508948	SK-N-SH	brain:	n/a	chr8:59508508-59508517 chr8:59508694-59508703
34	JUN	chr8:59508289-59508879	K562	blood:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
35	TBL1XR1	chr8:59508201-59508870	K562	blood:	n/a	n/a
36	TEAD4	chr8:59508410-59508809	K562	blood:	n/a	n/a
37	SP1	chr8:59508421-59508953	GM12878	blood:	n/a	n/a
38	EP300	chr8:59508339-59509015	GM12878	blood:	n/a	chr8:59508596-59508610 chr8:59508646-59508660 chr8:59508508-59508517
39	STAT3	chr8:59507900-59509004	GM12878	blood:	n/a	n/a
40	MYC	chr8:59508424-59508974	NB4	blood:	n/a	chr8:59508508-59508517 chr8:59508694-59508703
41	RCOR1	chr8:59508363-59509053	K562	blood:	n/a	n/a
42	CEBPB	chr8:59508391-59508904	IMR90	lung:	n/a	chr8:59508455-59508467
43	SP1	chr8:59508402-59508987	GM12878	blood:	n/a	n/a
44	EP300	chr8:59507804-59509165	SK-N-SH	brain:	n/a	chr8:59508596-59508610 chr8:59508646-59508660 chr8:59508508-59508517
45	STAT3	chr8:59508134-59508916	MCF10A-Er-Src	breast:	n/a	n/a
46	JUN	chr8:59508096-59508900	HUVEC	blood vessel:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
47	JUND	chr8:59508272-59509071	SK-N-SH	brain:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
48	GATA3	chr8:59507804-59509025	SK-N-SH	brain:	n/a	chr8:59508507-59508516
49	FOSL2	chr8:59508285-59509056	SK-N-SH	brain:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
50	MYC	chr8:59508423-59509098	K562	blood:	n/a	chr8:59508508-59508517 chr8:59508694-59508703

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:59508283..59510200-chr8:59512626..59515081,2	MCF-7	breast:
2	chr8:59507125..59509829-chr8:59569234..59572145,2	MCF-7	breast:

Variant related genes	Relation type
NSMAF	TF binding region
ENSG00000035681	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10086130	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10086457	0.94[ASN][1000 genomes]
rs10093782	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10098355	1.00[EUR][1000 genomes]
rs16923631	1.00[EUR][1000 genomes]
rs2054900	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2228505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28548238	1.00[EUR][1000 genomes]
rs3816847	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4737505	1.00[EUR][1000 genomes]
rs4738695	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4738696	0.92[ASN][1000 genomes]
rs55658192	0.92[ASN][1000 genomes]
rs58627447	1.00[EUR][1000 genomes]
rs58866790	1.00[EUR][1000 genomes]
rs60289621	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60504120	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60534391	0.94[ASN][1000 genomes]
rs60780937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991479	0.94[ASN][1000 genomes]
rs6991644	0.94[ASN][1000 genomes]
rs7816499	0.92[ASN][1000 genomes]
rs7841618	0.94[ASN][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	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv890939	chr8:59471187-59544413	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1031537	chr8:59482949-59536971	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv831325	chr8:59492580-59694443	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr8:59467400-59559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:59472800-59515800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:59473200-59508600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr8:59477600-59514200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:59477800-59508800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:59478000-59508600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr8:59478000-59508800	Strong transcription	Fetal Intestine Large	intestine
8	chr8:59480600-59515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr8:59483200-59508800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr8:59483800-59528000	Strong transcription	Dnd41	blood
11	chr8:59495200-59512800	Strong transcription	Fetal Muscle Leg	muscle
12	chr8:59498600-59511200	Weak transcription	Right Ventricle	heart
13	chr8:59498600-59511800	Weak transcription	Brain Germinal Matrix	brain
14	chr8:59498600-59548400	Weak transcription	Stomach Mucosa	stomach
15	chr8:59500200-59524600	Weak transcription	HepG2	liver
16	chr8:59500600-59521000	Weak transcription	Fetal Heart	heart
17	chr8:59500600-59528800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr8:59502000-59512800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr8:59503000-59545400	Weak transcription	Esophagus	oesophagus
20	chr8:59504200-59508600	Strong transcription	Fetal Thymus	thymus
21	chr8:59504400-59509200	Strong transcription	Liver	Liver
22	chr8:59504400-59510200	Strong transcription	Primary T cells from cord blood	blood
23	chr8:59505200-59510200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr8:59505200-59513000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr8:59505400-59508600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr8:59505400-59513000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr8:59505600-59511000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr8:59505600-59512800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr8:59505800-59510200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr8:59506000-59508600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr8:59506000-59508600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr8:59506000-59508800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr8:59506000-59509000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr8:59506000-59510800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr8:59506000-59513000	Strong transcription	Fetal Lung	lung
36	chr8:59506000-59516800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr8:59506200-59508800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr8:59506200-59508800	Genic enhancers	Fetal Brain Male	brain
39	chr8:59506200-59509200	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
40	chr8:59506200-59510200	Strong transcription	Brain Angular Gyrus	brain
41	chr8:59506200-59512000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr8:59506400-59508600	Genic enhancers	NHLF	lung
43	chr8:59506400-59508800	Strong transcription	Brain Cingulate Gyrus	brain
44	chr8:59506400-59509200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr8:59506400-59509200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
46	chr8:59506400-59509200	Genic enhancers	Fetal Brain Female	brain
47	chr8:59506400-59509400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr8:59506400-59509800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr8:59506400-59510400	Strong transcription	Thymus	Thymus
50	chr8:59506400-59513000	Strong transcription	Fetal Stomach	stomach

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