Variant report

Variant	rs56884277
Chromosome Location	chr17:16286623-16286624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:90)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:90 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:16286238-16288621	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr17:16285066-16289026	K562	blood:	n/a	n/a
3	BCLAF1	chr17:16286517-16287086	GM12878	blood:	n/a	chr17:16286751-16286760
4	POLR2A	chr17:16286360-16287058	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr17:16286007-16288677	K562	blood:	n/a	n/a
6	POLR2A	chr17:16286426-16287142	K562	blood:	n/a	n/a
7	POLR2A	chr17:16284108-16288378	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:16284186-16288304	GM12891	blood:	n/a	n/a
9	POU2F2	chr17:16286192-16287230	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:16286356-16287070	HCT-116	colon:	n/a	n/a
11	PML	chr17:16286497-16286980	K562	blood:	n/a	n/a
12	POLR2A	chr17:16286439-16286694	GM12878	blood:	n/a	n/a
13	POLR2A	chr17:16286293-16287171	U87	brain:	n/a	n/a
14	SPI1	chr17:16286543-16286911	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:16286508-16286800	H1-hESC	embryonic stem cell:	n/a	n/a
16	HEY1	chr17:16284242-16287123	K562	blood:	n/a	n/a
17	POLR2A	chr17:16286536-16286730	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr17:16286580-16286835	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:16286261-16288403	PFSK-1	brain:	n/a	n/a
20	SPI1	chr17:16286597-16286938	GM12891	blood:	n/a	n/a
21	STAT5A	chr17:16286499-16287577	GM12878	blood:	n/a	chr17:16286749-16286760
22	POLR2A	chr17:16286028-16287849	IMR90	lung:	n/a	n/a
23	POLR2A	chr17:16286083-16287049	A549	lung:	n/a	n/a
24	TEAD4	chr17:16286440-16287120	K562	blood:	n/a	n/a
25	POLR2A	chr17:16286436-16287122	U87	brain:	n/a	n/a
26	POLR2A	chr17:16286097-16286926	GM12878	blood:	n/a	n/a
27	POLR2A	chr17:16283607-16288791	HepG2	liver:	n/a	n/a
28	POLR2A	chr17:16286369-16288369	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr17:16286517-16287259	ECC-1	luminal epithelium:	n/a	n/a
30	USF2	chr17:16286492-16287136	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr17:16285958-16288532	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr17:16286401-16287101	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr17:16285985-16288536	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr17:16286495-16287072	HCT-116	colon:	n/a	n/a
35	POLR2A	chr17:16284143-16287328	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr17:16286009-16288538	GM12878	blood:	n/a	n/a
37	SPI1	chr17:16286617-16286878	GM12878	blood:	n/a	n/a
38	POLR2A	chr17:16286571-16287045	K562	blood:	n/a	n/a
39	POLR2A	chr17:16283735-16288202	GM12892	blood:	n/a	n/a
40	POLR2A	chr17:16286085-16287191	H1-hESC	embryonic stem cell:	n/a	n/a
41	HEY1	chr17:16286530-16287062	HepG2	liver:	n/a	n/a
42	POLR2A	chr17:16286422-16287639	Hela-S3	cervix:	n/a	n/a
43	NFATC1	chr17:16286436-16287146	GM12878	blood:	n/a	n/a
44	POLR2A	chr17:16286343-16287177	U87	brain:	n/a	n/a
45	BACH1	chr17:16286596-16286867	K562	blood:	n/a	n/a
46	POLR2A	chr17:16286555-16286723	A549	lung:	n/a	n/a
47	POLR2A	chr17:16286152-16286741	K562	blood:	n/a	n/a
48	POLR2A	chr17:16286367-16286998	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr17:16286523-16288732	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr17:16284231-16288225	GM12892	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:16282813..16296019-chr17:16339657..16347255,30	K562	blood:
2	chr17:16280844..16288183-chr17:16338320..16344372,17	MCF-7	breast:
3	chr17:16117769..16122024-chr17:16284027..16287393,3	K562	blood:
4	chr12:125395295..125399195-chr17:16283774..16286758,3	K562	blood:
5	chr17:16286008..16287647-chr17:16329953..16332431,2	MCF-7	breast:
6	chr17:16286242..16290489-chr17:16309075..16312817,4	K562	blood:
7	chr17:16285971..16289301-chr17:16317139..16320452,4	MCF-7	breast:
8	chr17:16282157..16292955-chr17:16316721..16324527,22	K562	blood:
9	chr17:16286179..16290055-chr17:16297586..16300314,3	K562	blood:
10	chr17:16282507..16286910-chr17:16340967..16348886,17	K562	blood:
11	chr17:16286607..16287114-chr2:85765893..85766478,2	NB4	blood:
12	chr17:16282005..16293050-chr17:16338399..16351573,30	MCF-7	breast:
13	chr17:16282157..16291704-chr17:16317315..16324527,14	K562	blood:
14	chr17:16286568..16288950-chr17:16335922..16337918,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265401	TF binding region
ENSG00000266651	Chromatin interaction
ENSG00000141027	Chromatin interaction
ENSG00000239203	Chromatin interaction
ENSG00000175061	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000108474	Chromatin interaction
ENSG00000150991	Chromatin interaction
ENSG00000187688	Chromatin interaction
ENSG00000264739	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs28610260	0.81[ASN][1000 genomes]
rs28833845	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60865756	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065945	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9893057	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9893097	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908067	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908960	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS 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 miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv1065254	chr17:16252880-16389930	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
9	nsv428668	chr17:16265210-16455285	Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
10	nsv978556	chr17:16268432-16302479	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 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	chr17:16284600-16287000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
2	chr17:16284800-16287600	Transcr. at gene 5' and 3'	A549	lung
3	chr17:16285000-16287000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr17:16285000-16287000	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
5	chr17:16285000-16287000	Transcr. at gene 5' and 3'	Fetal Lung	lung
6	chr17:16285000-16287000	Transcr. at gene 5' and 3'	NH-A	brain
7	chr17:16285000-16287200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:16285000-16288200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr17:16285200-16286800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
10	chr17:16285200-16287000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:16285200-16287000	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
12	chr17:16285200-16287000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
13	chr17:16285200-16287000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
14	chr17:16285200-16287000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
15	chr17:16285200-16287000	Transcr. at gene 5' and 3'	HSMM	muscle
16	chr17:16285200-16287000	Transcr. at gene 5' and 3'	Osteobl	bone
17	chr17:16285200-16287400	Transcr. at gene 5' and 3'	Thymus	Thymus
18	chr17:16285200-16287600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
19	chr17:16285400-16287000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr17:16285400-16287000	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr17:16285400-16287000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr17:16285400-16287200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr17:16285400-16287200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr17:16285400-16287200	Strong transcription	Lung	lung
25	chr17:16285400-16287200	Transcr. at gene 5' and 3'	Hela-S3	cervix
26	chr17:16285400-16287400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:16285400-16287400	Genic enhancers	Placenta	Placenta
28	chr17:16285400-16288200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
29	chr17:16285400-16289600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr17:16285400-16289800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:16285600-16286800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr17:16285600-16287000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr17:16285600-16287000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr17:16285600-16287000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr17:16285600-16287000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
36	chr17:16285600-16287000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr17:16285600-16287000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr17:16285600-16287000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr17:16285600-16287000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr17:16285600-16287000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr17:16285600-16287000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr17:16285600-16287000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
43	chr17:16285600-16287000	Strong transcription	Ovary	ovary
44	chr17:16285600-16287000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
45	chr17:16285600-16287000	Genic enhancers	Monocytes-CD14+_RO01746	blood
46	chr17:16285600-16287200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr17:16285600-16287200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr17:16285600-16287200	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr17:16285600-16287200	Genic enhancers	Left Ventricle	heart
50	chr17:16285600-16287400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links