Variant report

Variant	rs28587878
Chromosome Location	chr8:62623504-62623505
allele	G/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	POLR2A	chr8:62623377-62623799	SK-N-MC	brain:	n/a	n/a
2	SMC3	chr8:62623010-62624059	SK-N-SH	brain:	n/a	chr8:62623706-62623720
3	RAD21	chr8:62623420-62623916	MCF-7	breast:	n/a	chr8:62623711-62623720 chr8:62623702-62623721
4	POLR2A	chr8:62620749-62628224	U87	brain:	n/a	n/a
5	FOXA2	chr8:62623440-62623946	A549	lung:	n/a	chr8:62623824-62623836
6	BCL3	chr8:62622937-62626728	A549	lung:	n/a	chr8:62622975-62622984 chr8:62623067-62623076 chr8:62626676-62626685
7	CEBPB	chr8:62622909-62623992	A549	lung:	n/a	chr8:62623272-62623283
8	POLR2A	chr8:62621167-62627994	A549	lung:	n/a	n/a
9	RAD21	chr8:62623087-62623902	IMR90	lung:	n/a	chr8:62623711-62623720 chr8:62623702-62623721
10	FOXA1	chr8:62623240-62623887	HepG2	liver:	n/a	chr8:62623824-62623836 chr8:62623750-62623765
11	STAT3	chr8:62622945-62623655	MCF10A-Er-Src	breast:	n/a	chr8:62623065-62623076
12	RFX5	chr8:62623476-62623853	K562	blood:	n/a	n/a
13	CTCF	chr8:62623417-62623997	HCT-116	colon:	n/a	chr8:62623705-62623721 chr8:62623699-62623720 chr8:62623704-62623722 chr8:62623711-62623718 chr8:62623653-62623661
14	FOS	chr8:62623070-62623748	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr8:62623083-62623843	K562	blood:	n/a	chr8:62623272-62623283
16	RCOR1	chr8:62623414-62623868	K562	blood:	n/a	n/a
17	RAD21	chr8:62623496-62623824	SK-N-SH_RA	brain:	n/a	chr8:62623711-62623720 chr8:62623702-62623721
18	FOS	chr8:62623105-62623800	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr8:62623280-62623925	K562	blood:	n/a	n/a
20	POLR2A	chr8:62620948-62624035	U87	brain:	n/a	n/a
21	EBF1	chr8:62623119-62623937	GM12878	blood:	n/a	n/a
22	CTCF	chr8:62623484-62623949	MCF-7	breast:	n/a	chr8:62623705-62623721 chr8:62623699-62623720 chr8:62623704-62623722 chr8:62623711-62623718 chr8:62623653-62623661
23	RAD21	chr8:62623399-62624029	HCT-116	colon:	n/a	chr8:62623711-62623720 chr8:62623702-62623721
24	CTCF	chr8:62623379-62624276	IMR90	lung:	n/a	chr8:62623705-62623721 chr8:62623699-62623720 chr8:62623704-62623722 chr8:62623711-62623718 chr8:62623653-62623661
25	TCF12	chr8:62622969-62628409	A549	lung:	n/a	n/a
26	CTCF	chr8:62623490-62623864	A549	lung:	n/a	chr8:62623705-62623721 chr8:62623699-62623720 chr8:62623704-62623722 chr8:62623711-62623718 chr8:62623653-62623661
27	ATF3	chr8:62623320-62624096	A549	lung:	n/a	n/a
28	RAD21	chr8:62623263-62623912	GM12878	blood:	n/a	chr8:62623711-62623720 chr8:62623702-62623721
29	PRDM1	chr8:62623004-62623795	Hela-S3	cervix:	n/a	chr8:62623063-62623077 chr8:62623064-62623077 chr8:62623064-62623073
30	CTCF	chr8:62623334-62623915	K562	blood:	n/a	chr8:62623705-62623721 chr8:62623699-62623720 chr8:62623704-62623722 chr8:62623711-62623718 chr8:62623653-62623661
31	SIX5	chr8:62622210-62626661	A549	lung:	n/a	chr8:62624442-62624451
32	GTF2F1	chr8:62623079-62623935	Hela-S3	cervix:	n/a	n/a
33	FOSL2	chr8:62622834-62624069	A549	lung:	n/a	chr8:62624031-62624043
34	STAT3	chr8:62623292-62623912	Hela-S3	cervix:	n/a	n/a
35	FOS	chr8:62623089-62623849	MCF10A-Er-Src	breast:	n/a	n/a
36	CEBPB	chr8:62623062-62623866	Hela-S3	cervix:	n/a	chr8:62623272-62623283
37	CTCF	chr8:62623500-62623650	A549	lung:	n/a	n/a
38	RAD21	chr8:62623500-62623877	ECC-1	luminal epithelium:	n/a	chr8:62623711-62623720 chr8:62623702-62623721
39	RAD21	chr8:62623497-62623960	ECC-1	luminal epithelium:	n/a	chr8:62623711-62623720 chr8:62623702-62623721
40	MYC	chr8:62623108-62623865	MCF10A-Er-Src	breast:	n/a	n/a
41	EP300	chr8:62622743-62623871	Hela-S3	cervix:	n/a	chr8:62623823-62623833 chr8:62623751-62623761 chr8:62623269-62623283
42	MYBL2	chr8:62623434-62623972	HepG2	liver:	n/a	n/a
43	CEBPB	chr8:62623498-62623796	K562	blood:	n/a	n/a
44	EP300	chr8:62622946-62628108	A549	lung:	n/a	chr8:62626370-62626379 chr8:62627005-62627021 chr8:62627011-62627027 chr8:62624213-62624227 chr8:62624029-62624043 chr8:62625613-62625627 chr8:62623823-62623833 chr8:62623751-62623761 chr8:62625013-62625021 chr8:62623269-62623283 chr8:62627288-62627304 chr8:62627012-62627028 chr8:62627697-62627706 chr8:62624040-62624054 chr8:62627488-62627504
45	POLR2A	chr8:62620561-62626562	K562	blood:	n/a	n/a
46	BRCA1	chr8:62622929-62623955	Hela-S3	cervix:	n/a	n/a
47	BATF	chr8:62623071-62623557	GM12878	blood:	n/a	n/a
48	MYC	chr8:62623215-62623814	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr8:62620532-62628356	U87	brain:	n/a	n/a
50	POLR2A	chr8:62623504-62623889	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:62620828..62625218-chr8:62625341..62628340,6	MCF-7	breast:
2	chr8:62560140..62569925-chr8:62619825..62628019,19	K562	blood:
3	chr8:62565425..62565962-chr8:62623306..62624081,2	MCF-7	breast:
4	chr8:62612675..62615533-chr8:62623174..62625946,2	MCF-7	breast:
5	chr8:62618042..62628934-chr8:62666240..62683608,38	K562	blood:
6	chr8:62605925..62608885-chr8:62622452..62624247,2	MCF-7	breast:
7	chr8:62621847..62624556-chr8:62711277..62713553,2	K562	blood:
8	chr8:62538409..62541040-chr8:62622650..62625118,2	K562	blood:
9	chr8:62620081..62623599-chr8:62678566..62680861,4	K562	blood:
10	chr8:62622252..62623796-chr8:64080473..64083451,2	K562	blood:
11	chr8:62619459..62621551-chr8:62623294..62626246,2	MCF-7	breast:
12	chr8:62597423..62607954-chr8:62618870..62628159,21	K562	blood:
13	chr8:62567262..62573065-chr8:62621554..62624953,7	K562	blood:
14	chr8:62564124..62567084-chr8:62621412..62624391,3	MCF-7	breast:

Variant related genes	Relation type
MIR4470	TF binding region
ENSG00000264408	Chromatin interaction
ENSG00000251127	Chromatin interaction
ENSG00000270673	Chromatin interaction
ENSG00000185728	Chromatin interaction
ENSG00000198363	Chromatin interaction

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

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

rs_ID	r²[population]
rs10095911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10107157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13439225	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28793942	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3195249	1.00[EUR][1000 genomes]
rs73269297	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73269300	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73269302	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73271212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73271213	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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	nsv1024432	chr8:62086247-62898782	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv932198	chr8:62336705-62914562	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2761430	chr8:62517980-62873803	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1015216	chr8:62517980-62873803	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:62610000-62624400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr8:62613000-62624600	Weak transcription	Brain Germinal Matrix	brain
3	chr8:62613000-62626400	Weak transcription	Lung	lung
4	chr8:62613800-62624600	Weak transcription	Left Ventricle	heart
5	chr8:62613800-62624600	Weak transcription	Right Ventricle	heart
6	chr8:62613800-62624600	Weak transcription	Thymus	Thymus
7	chr8:62614000-62624400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:62617600-62624000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:62617800-62624400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr8:62618400-62624600	Enhancers	Rectal Smooth Muscle	rectum
11	chr8:62618600-62624200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr8:62619200-62624600	Weak transcription	Fetal Thymus	thymus
13	chr8:62619200-62625000	Enhancers	Fetal Heart	heart
14	chr8:62620000-62623600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:62620000-62623600	Transcr. at gene 5' and 3'	A549	lung
16	chr8:62620000-62624400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr8:62620000-62624600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr8:62620200-62624600	Enhancers	Primary hematopoietic stem cells	blood
19	chr8:62620400-62623600	Enhancers	HSMMtube	muscle
20	chr8:62620600-62623600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr8:62620600-62624200	Enhancers	HSMM	muscle
22	chr8:62620800-62623800	Enhancers	HUVEC	blood vessel
23	chr8:62620800-62624000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr8:62620800-62624200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr8:62621000-62623600	Flanking Active TSS	NH-A	brain
26	chr8:62621000-62624200	Enhancers	Liver	Liver
27	chr8:62621200-62624200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr8:62621200-62624200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr8:62621400-62624200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr8:62621600-62624200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr8:62621800-62624400	Weak transcription	Fetal Stomach	stomach
32	chr8:62621800-62624600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr8:62622000-62624600	Enhancers	Fetal Intestine Small	intestine
34	chr8:62622200-62624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr8:62622200-62624600	Weak transcription	Aorta	Aorta
36	chr8:62622200-62624600	Weak transcription	Ovary	ovary
37	chr8:62622200-62624600	Weak transcription	Psoas Muscle	Psoas
38	chr8:62622200-62626200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr8:62622200-62626200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr8:62622200-62626200	Weak transcription	Pancreas	Pancrea
41	chr8:62622200-62626400	Weak transcription	Gastric	stomach
42	chr8:62622400-62624200	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr8:62622400-62626000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr8:62622400-62627800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr8:62622600-62623600	Flanking Active TSS	HepG2	liver
46	chr8:62622600-62625800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr8:62622800-62623600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:62622800-62623600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr8:62622800-62623600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr8:62622800-62623800	Enhancers	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links