Variant report

Variant	rs1689513
Chromosome Location	chr12:56509386-56509387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56508868-56512664	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:56509337-56509423	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:56509018-56509486	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:56508987-56509510	GM12892	blood:	n/a	n/a
5	STAT3	chr12:56509216-56509596	MCF10A-Er-Src	breast:	n/a	chr12:56509400-56509408
6	POLR2A	chr12:56508873-56512706	U87	brain:	n/a	n/a
7	POLR2A	chr12:56509267-56509453	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:56509084-56511359	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr12:56509096-56509463	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:56508976-56509891	MCF-7	breast:	n/a	n/a
11	POLR2A	chr12:56508985-56513679	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:56509088-56509911	HCT-116	colon:	n/a	n/a
13	POLR2A	chr12:56508762-56509420	K562	blood:	n/a	n/a
14	POLR2A	chr12:56507127-56512673	PFSK-1	brain:	n/a	n/a
15	SETDB1	chr12:56507833-56510301	K562	blood:	n/a	chr12:56510089-56510113
16	FOS	chr12:56509218-56509505	MCF10A-Er-Src	breast:	n/a	n/a
17	CHD1	chr12:56509278-56509515	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:56509008-56512584	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr12:56508835-56512388	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr12:56509196-56509546	MCF10A-Er-Src	breast:	n/a	chr12:56509400-56509408
21	POLR2A	chr12:56509102-56509432	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr12:56509281-56509401	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:56508619-56512952	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr12:56508960-56511348	ECC-1	luminal epithelium:	n/a	n/a
25	CREB1	chr12:56509205-56511233	H1-hESC	embryonic stem cell:	n/a	n/a
26	FOS	chr12:56509211-56509481	MCF10A-Er-Src	breast:	n/a	n/a
27	MTA3	chr12:56508902-56511281	GM12878	blood:	n/a	n/a
28	TAF1	chr12:56509178-56509471	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:56509151-56512697	Hela-S3	cervix:	n/a	n/a
30	SIX5	chr12:56509201-56511424	A549	lung:	n/a	chr12:56510707-56510721
31	POLR2A	chr12:56508896-56514071	SK-N-MC	brain:	n/a	n/a
32	PML	chr12:56509300-56511364	GM12878	blood:	n/a	n/a
33	SETDB1	chr12:56509033-56510606	K562	blood:	n/a	chr12:56510089-56510113
34	HCFC1	chr12:56508835-56511266	Hela-S3	cervix:	n/a	n/a
35	YY1	chr12:56509353-56511031	SK-N-SH	brain:	n/a	chr12:56510068-56510078
36	POLR2A	chr12:56508570-56511353	PANC-1	pancreas:	n/a	n/a
37	STAT3	chr12:56509231-56509620	MCF10A-Er-Src	breast:	n/a	chr12:56509400-56509408
38	POLR2A	chr12:56509111-56509852	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr12:56508873-56511389	U87	brain:	n/a	n/a
40	POLR2A	chr12:56509179-56509507	HL-60	blood:	n/a	n/a
41	POLR2A	chr12:56509126-56509697	Hela-S3	cervix:	n/a	n/a
42	USF1	chr12:56509351-56510999	A549	lung:	n/a	n/a
43	SETDB1	chr12:56509200-56509626	U2OS	brain:	n/a	n/a
44	MYC	chr12:56509012-56509541	MCF10A-Er-Src	breast:	n/a	n/a
45	TCF12	chr12:56509269-56511338	A549	lung:	n/a	chr12:56509401-56509409
46	CBX3	chr12:56509081-56510716	K562	blood:	n/a	n/a
47	POLR2A	chr12:56506630-56509471	PFSK-1	brain:	n/a	n/a
48	FOS	chr12:56509271-56509522	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr12:56509080-56512855	GM12891	blood:	n/a	n/a
50	KAP1	chr12:56508738-56511155	K562	blood:	n/a	n/a

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56388663..56390972-chr12:56509029..56512021,2	K562	blood:
2	chr12:56364310..56368149-chr12:56508797..56512267,4	K562	blood:
3	chr12:56471198..56482935-chr12:56506922..56516262,73	MCF-7	breast:
4	chr12:56434006..56443603-chr12:56507645..56514884,44	K562	blood:
5	chr12:56507991..56525761-chr12:56579808..56586137,68	MCF-7	breast:
6	chr12:56470948..56480058-chr12:56507665..56513741,17	K562	blood:
7	chr12:56433777..56443620-chr12:56502225..56514736,38	MCF-7	breast:
8	chr12:56508832..56515879-chr12:56578376..56587782,37	MCF-7	breast:
9	chr12:56433331..56443603-chr12:56506173..56514581,35	K562	blood:
10	chr12:56508592..56516532-chr12:56613723..56619321,16	MCF-7	breast:
11	chr12:56509088..56512395-chr12:56615837..56618663,6	MCF-7	breast:
12	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
13	chr12:56485826..56488734-chr12:56509000..56512057,4	MCF-7	breast:
14	chr12:56508549..56510968-chr12:56650635..56652672,2	K562	blood:
15	chr12:56364840..56368363-chr12:56508725..56511034,3	MCF-7	breast:
16	chr12:56365214..56370075-chr12:56508797..56513405,7	K562	blood:
17	chr12:56509109..56511870-chr12:58238772..58240512,2	MCF-7	breast:
18	chr12:56509009..56513573-chr12:56543891..56549811,15	MCF-7	breast:
19	chr12:56509108..56511988-chr12:56607579..56610265,3	MCF-7	breast:
20	chr12:56120734..56123554-chr12:56508983..56512643,4	K562	blood:
21	chr12:56120240..56124369-chr12:56508983..56513755,7	K562	blood:
22	chr12:56509186..56511595-chr17:57696618..57699149,2	MCF-7	breast:
23	chr12:56509168..56511032-chr8:89338903..89341041,2	MCF-7	breast:
24	chr12:56384934..56392097-chr12:56507991..56512680,9	MCF-7	breast:
25	chr12:56509253..56512129-chr20:48805699..48808212,2	MCF-7	breast:
26	chr12:56433908..56446518-chr12:56506026..56517165,55	MCF-7	breast:
27	chr12:56508809..56510764-chr12:56599083..56602817,4	K562	blood:
28	chr12:56390533..56392803-chr12:56508864..56512540,5	K562	blood:
29	chr12:56509359..56512044-chr12:56694319..56695939,2	MCF-7	breast:
30	chr12:56508870..56510876-chr8:144821335..144824118,2	MCF-7	breast:
31	chr12:56509293..56514359-chr12:56692717..56696999,9	K562	blood:
32	chr12:56122088..56125310-chr12:56509016..56512267,4	MCF-7	breast:
33	chr12:56415006..56416530-chr12:56508987..56510666,2	K562	blood:
34	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
35	chr12:56509092..56510764-chr12:56601288..56602817,2	K562	blood:

No data

Variant related genes	Relation type
ZC3H10	TF binding region
RPL41	TF binding region
ESYT1	TF binding region
ENSG00000257553	TF binding region
ENSG00000123374	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000255990	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000253553	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000141367	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000156103	Chromatin interaction
ENSG00000172216	Chromatin interaction
ENSG00000139645	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1274298	1.00[ASN][1000 genomes]
rs12810816	1.00[ASN][1000 genomes]
rs1290898	1.00[ASN][1000 genomes]
rs17118313	1.00[ASN][1000 genomes]
rs34457402	1.00[ASN][1000 genomes]
rs35436573	1.00[ASN][1000 genomes]
rs703822	1.00[ASW][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs705703	1.00[ASW][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs705707	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73340323	1.00[ASN][1000 genomes]
rs773121	1.00[ASN][1000 genomes]
rs773122	1.00[ASN][1000 genomes]
rs773123	1.00[ASN][1000 genomes]
rs773643	1.00[ASN][1000 genomes]
rs773645	1.00[ASN][1000 genomes]
rs773649	1.00[ASN][1000 genomes]
rs773662	1.00[ASN][1000 genomes]
rs7958618	1.00[ASN][1000 genomes]
rs7977273	1.00[ASN][1000 genomes]
rs812826	1.00[ASN][1000 genomes]
rs812842	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 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	chr12:56499200-56509600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56504800-56509600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56506600-56509400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:56506600-56510000	Weak transcription	Gastric	stomach
5	chr12:56507000-56509400	Weak transcription	Colonic Mucosa	Colon
6	chr12:56507600-56509400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:56507600-56510000	Weak transcription	Spleen	Spleen
8	chr12:56507800-56509400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:56507800-56509400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:56507800-56509600	Weak transcription	Fetal Lung	lung
11	chr12:56508000-56509400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:56508000-56509400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:56508000-56509400	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:56508000-56509600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:56508000-56509600	Weak transcription	HSMMtube	muscle
16	chr12:56508400-56509400	Weak transcription	Primary T cells from cord blood	blood
17	chr12:56508400-56509600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:56508400-56510000	Weak transcription	K562	blood
19	chr12:56508800-56509400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:56509000-56509400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:56509000-56509400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:56509000-56509400	Enhancers	Primary B cells from peripheral blood	blood
23	chr12:56509000-56509400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:56509000-56509400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr12:56509000-56509400	Flanking Active TSS	HMEC	breast
26	chr12:56509000-56509400	Flanking Active TSS	NHEK	skin
27	chr12:56509000-56509600	Flanking Active TSS	Osteobl	bone
28	chr12:56509000-56510400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:56509000-56510600	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr12:56509000-56510600	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr12:56509000-56510800	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr12:56509000-56510800	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr12:56509000-56511000	Active TSS	H1 Cell Line	embryonic stem cell
34	chr12:56509000-56511600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:56509000-56512400	Active TSS	Brain Angular Gyrus	brain
36	chr12:56509000-56512800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr12:56509000-56513400	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr12:56509200-56509400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:56509200-56509400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:56509200-56509400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:56509200-56509400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:56509200-56509400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:56509200-56509400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:56509200-56509400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr12:56509200-56509400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr12:56509200-56509400	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:56509200-56509400	Enhancers	Primary B cells from cord blood	blood
48	chr12:56509200-56509400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:56509200-56509400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr12:56509200-56509400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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