Variant report

Variant	rs3802996
Chromosome Location	chr12:56512258-56512259
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	POLR2A	chr12:56509991-56512745	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:56508868-56512664	HepG2	liver:	n/a	n/a
3	NFIC	chr12:56511463-56512300	GM12878	blood:	n/a	n/a
4	USF2	chr12:56511709-56512334	GM12878	blood:	n/a	chr12:56512065-56512081 chr12:56512156-56512172 chr12:56512089-56512105
5	SP2	chr12:56511630-56512325	HepG2	liver:	n/a	chr12:56511833-56511842
6	POLR2A	chr12:56511544-56512672	K562	blood:	n/a	n/a
7	SIN3AK20	chr12:56511526-56512642	HCT-116	colon:	n/a	n/a
8	POLR2A	chr12:56510091-56512565	Hela-S3	cervix:	n/a	n/a
9	E2F6	chr12:56511527-56512562	A549	lung:	n/a	chr12:56512436-56512443 chr12:56512093-56512103 chr12:56511799-56511813 chr12:56512090-56512100 chr12:56511803-56511811 chr12:56512108-56512120 chr12:56512282-56512291 chr12:56511803-56511811 chr12:56512109-56512120 chr12:56512349-56512363 chr12:56512284-56512293 chr12:56512436-56512443 chr12:56511815-56511826 chr12:56512436-56512443
10	YY1	chr12:56511584-56512368	GM12878	blood:	n/a	chr12:56512089-56512103 chr12:56512130-56512144 chr12:56512089-56512098 chr12:56512148-56512162
11	SIN3AK20	chr12:56511584-56512629	MCF-7	breast:	n/a	n/a
12	EP300	chr12:56511560-56512459	ECC-1	luminal epithelium:	n/a	chr12:56512066-56512082 chr12:56512091-56512100 chr12:56512088-56512097
13	SP4	chr12:56511534-56512539	H1-hESC	embryonic stem cell:	n/a	chr12:56511830-56511846
14	EP300	chr12:56511497-56512514	A549	lung:	n/a	chr12:56512066-56512082 chr12:56512091-56512100 chr12:56512088-56512097
15	SP4	chr12:56511507-56512410	H1-hESC	embryonic stem cell:	n/a	chr12:56511830-56511846
16	MYC	chr12:56511731-56512313	MCF-7	breast:	n/a	chr12:56511899-56511908
17	POLR2A	chr12:56511615-56512434	A549	lung:	n/a	n/a
18	TAF1	chr12:56511220-56512587	Hela-S3	cervix:	n/a	n/a
19	JUND	chr12:56511533-56512402	SK-N-SH	brain:	n/a	chr12:56512107-56512116 chr12:56512283-56512292
20	BHLHE40	chr12:56511612-56512417	GM12878	blood:	n/a	chr12:56512065-56512081 chr12:56512156-56512172 chr12:56512089-56512105
21	POLR2A	chr12:56511520-56512488	SK-N-SH	brain:	n/a	n/a
22	MYC	chr12:56511670-56512341	MCF-7	breast:	n/a	chr12:56511899-56511908
23	IRF1	chr12:56511672-56512347	K562	blood:	n/a	chr12:56511828-56511842
24	CREB1	chr12:56511552-56512744	HepG2	liver:	n/a	chr12:56512281-56512294
25	TAF7	chr12:56511503-56512644	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr12:56511454-56512474	PANC-1	pancreas:	n/a	n/a
27	TAF1	chr12:56511477-56512602	ECC-1	luminal epithelium:	n/a	n/a
28	CCNT2	chr12:56511680-56512356	K562	blood:	n/a	n/a
29	BCLAF1	chr12:56511480-56512333	K562	blood:	n/a	chr12:56512089-56512102 chr12:56512090-56512099 chr12:56512092-56512105
30	GATA3	chr12:56511528-56512592	MCF-7	breast:	n/a	n/a
31	POLR2A	chr12:56511555-56512445	HEK293	kidney:	n/a	n/a
32	POLR2A	chr12:56511574-56512587	GM18526	blood:	n/a	n/a
33	POLR2A	chr12:56509992-56512562	GM12878	blood:	n/a	n/a
34	ATF2	chr12:56511516-56512503	GM12878	blood:	n/a	chr12:56512282-56512293 chr12:56512280-56512294
35	YY1	chr12:56511563-56512542	HepG2	liver:	n/a	chr12:56512089-56512103 chr12:56512130-56512144 chr12:56512089-56512098 chr12:56512148-56512162
36	FOXA1	chr12:56511624-56512266	HepG2	liver:	n/a	n/a
37	GABPA	chr12:56511513-56512686	A549	lung:	n/a	chr12:56512018-56512025
38	JUND	chr12:56511500-56512637	MCF-7	breast:	n/a	chr12:56512107-56512116 chr12:56512283-56512292
39	BACH1	chr12:56511613-56512273	K562	blood:	n/a	n/a
40	PML	chr12:56511546-56512387	GM12878	blood:	n/a	n/a
41	PBX3	chr12:56511598-56512514	SK-N-SH	brain:	n/a	n/a
42	SP2	chr12:56511630-56512296	HepG2	liver:	n/a	chr12:56511833-56511842
43	MXI1	chr12:56511529-56513939	SK-N-SH	brain:	n/a	chr12:56511899-56511914 chr12:56513357-56513366 chr12:56511850-56511865 chr12:56511897-56511912
44	GABPA	chr12:56511485-56512851	MCF-7	breast:	n/a	chr12:56512018-56512025
45	PBX3	chr12:56511589-56512519	SK-N-SH	brain:	n/a	n/a
46	SIN3AK20	chr12:56511618-56512588	PANC-1	pancreas:	n/a	n/a
47	FOSL2	chr12:56511542-56512566	MCF-7	breast:	n/a	chr12:56512107-56512116 chr12:56512283-56512292
48	SIN3A	chr12:56511568-56513589	H1-hESC	embryonic stem cell:	n/a	chr12:56512157-56512170
49	CTCF	chr12:56511808-56512384	K562	blood:	n/a	chr12:56512065-56512078
50	BCL3	chr12:56511471-56512643	A549	lung:	n/a	chr12:56512089-56512102 chr12:56512090-56512099 chr12:56512092-56512105

No.	Distal block	Cell Line	Cell type
1	chr12:56364310..56368149-chr12:56508797..56512267,4	K562	blood:
2	chr12:56471198..56482935-chr12:56506922..56516262,73	MCF-7	breast:
3	chr12:56208394..56211844-chr12:56510539..56512389,3	MCF-7	breast:
4	chr12:56510204..56512545-chr12:56576021..56578034,3	MCF-7	breast:
5	chr12:56434006..56443603-chr12:56507645..56514884,44	K562	blood:
6	chr12:56507991..56525761-chr12:56579808..56586137,68	MCF-7	breast:
7	chr12:56511703..56512580-chr17:36858507..36859419,3	Hela-S3	cervix:
8	chr12:56510693..56513436-chr12:56864879..56866666,2	K562	blood:
9	chr12:56470948..56480058-chr12:56507665..56513741,17	K562	blood:
10	chr12:56433777..56443620-chr12:56502225..56514736,38	MCF-7	breast:
11	chr12:56508832..56515879-chr12:56578376..56587782,37	MCF-7	breast:
12	chr12:56433331..56443603-chr12:56506173..56514581,35	K562	blood:
13	chr12:56508592..56516532-chr12:56613723..56619321,16	MCF-7	breast:
14	chr12:56512107..56514079-chr17:56708075..56709666,3	MCF-7	breast:
15	chr12:56399990..56402705-chr12:56510349..56512541,3	K562	blood:
16	chr12:56510333..56513421-chr12:56649218..56653989,6	MCF-7	breast:
17	chr12:56509088..56512395-chr12:56615837..56618663,6	MCF-7	breast:
18	chr12:56510352..56514795-chr12:56658341..56663841,11	K562	blood:
19	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
20	chr12:56510082..56512448-chr12:56678488..56681005,3	MCF-7	breast:
21	chr12:56115003..56117431-chr12:56512002..56513619,2	MCF-7	breast:
22	chr12:56510450..56514790-chr12:56614310..56619055,13	K562	blood:
23	chr12:56365214..56370075-chr12:56508797..56513405,7	K562	blood:
24	chr12:56511355..56512308-chr17:46703540..46704047,2	NB4	blood:
25	chr12:56509009..56513573-chr12:56543891..56549811,15	MCF-7	breast:
26	chr12:56120734..56123554-chr12:56508983..56512643,4	K562	blood:
27	chr12:56511043..56513292-chr12:56659388..56662092,2	MCF-7	breast:
28	chr12:56120240..56124369-chr12:56508983..56513755,7	K562	blood:
29	chr12:56367291..56369317-chr12:56511670..56513322,2	MCF-7	breast:
30	chr12:56384934..56392097-chr12:56507991..56512680,9	MCF-7	breast:
31	chr12:56511321..56512580-chr6:45345090..45346296,3	Hela-S3	cervix:
32	chr12:56433908..56446518-chr12:56506026..56517165,55	MCF-7	breast:
33	chr12:56357871..56361008-chr12:56510432..56513466,3	K562	blood:
34	chr12:56511670..56513648-chr17:41150005..41151671,2	K562	blood:
35	chr12:56509441..56516191-chr12:56612345..56620104,13	K562	blood:
36	chr12:56390533..56392803-chr12:56508864..56512540,5	K562	blood:
37	chr12:56510432..56513698-chr12:56649639..56653061,6	K562	blood:
38	chr12:56510402..56512934-chr17:58164381..58166726,2	MCF-7	breast:
39	chr12:56400915..56403340-chr12:56510572..56513192,4	MCF-7	breast:
40	chr12:56383086..56385013-chr12:56510688..56513350,2	K562	blood:
41	chr12:56510236..56513593-chr12:56624409..56626987,3	K562	blood:
42	chr12:56510786..56513733-chr12:56999811..57001767,2	K562	blood:
43	chr12:56136330..56139191-chr12:56511663..56513514,2	K562	blood:
44	chr12:56510939..56514946-chr12:56660063..56663348,9	K562	blood:
45	chr12:56382696..56386085-chr12:56510688..56513603,3	K562	blood:
46	chr12:56509293..56514359-chr12:56692717..56696999,9	K562	blood:
47	chr12:56122088..56125310-chr12:56509016..56512267,4	MCF-7	breast:
48	chr1:236443809..236446424-chr12:56511218..56513567,2	K562	blood:
49	chr12:56511802..56513894-chr12:56582502..56584213,17	K562	blood:
50	chr12:56399990..56401630-chr12:56510349..56512475,2	K562	blood:

Variant related genes	Relation type
ENSG00000257553	TF binding region
ENSG00000261040	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000255990	Chromatin interaction
ENSG00000200127	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000148516	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000135605	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000131469	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000265930	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000170689	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000196284	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000261005	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000139540	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000237036	Chromatin interaction
ENSG00000135437	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000272057	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000086619	Chromatin interaction
ENSG00000258056	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10747763	1.00[JPT][hapmap]
rs10876878	0.83[ASN][1000 genomes]
rs11171752	0.94[ASN][1000 genomes]
rs11171772	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11171777	1.00[JPT][hapmap]
rs11834728	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12320265	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1274502	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1274503	0.83[ASN][1000 genomes]
rs1405859	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17118333	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2271188	1.00[ASN][1000 genomes]
rs2271190	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2271192	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2463365	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2629451	0.83[ASN][1000 genomes]
rs2629453	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2695783	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2695784	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28676339	1.00[ASN][1000 genomes]
rs2930788	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2950573	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3759096	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3809130	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4759218	1.00[JPT][hapmap]
rs55887836	0.93[ASN][1000 genomes]
rs56851901	1.00[ASN][1000 genomes]
rs57280585	1.00[ASN][1000 genomes]
rs58009483	0.83[ASN][1000 genomes]
rs58476735	1.00[ASN][1000 genomes]
rs58548156	1.00[ASN][1000 genomes]
rs58663297	1.00[ASN][1000 genomes]
rs59053322	0.83[ASN][1000 genomes]
rs59078852	0.83[ASN][1000 genomes]
rs59966703	0.83[ASN][1000 genomes]
rs60396934	1.00[ASN][1000 genomes]
rs61939011	0.83[ASN][1000 genomes]
rs6581091	1.00[JPT][hapmap]
rs703823	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7311008	1.00[JPT][hapmap]
rs7489249	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs773654	0.83[ASN][1000 genomes]
rs773658	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs773659	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs773661	0.83[ASN][1000 genomes]
rs7962107	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7967464	0.83[ASN][1000 genomes]
rs7975405	0.83[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	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
4	nsv973076	chr12:56511030-56512707	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	86 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	chr12:56509000-56512400	Active TSS	Brain Angular Gyrus	brain
2	chr12:56509000-56512800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr12:56509000-56513400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:56509200-56512400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:56509200-56512600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:56509200-56512600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:56509200-56512600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:56509200-56512600	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr12:56509200-56512800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:56509200-56513000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:56509200-56513000	Active TSS	Lung	lung
12	chr12:56509400-56512400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:56509400-56512400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:56509400-56512400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr12:56509400-56512400	Active TSS	Colonic Mucosa	Colon
16	chr12:56509400-56512400	Active TSS	Colon Smooth Muscle	Colon
17	chr12:56509400-56512400	Active TSS	Fetal Heart	heart
18	chr12:56509400-56512400	Active TSS	Pancreas	Pancrea
19	chr12:56509400-56512400	Active TSS	Right Ventricle	heart
20	chr12:56509400-56512400	Active TSS	NHLF	lung
21	chr12:56509400-56512600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:56509400-56512600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr12:56509400-56512600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:56509400-56512600	Active TSS	Psoas Muscle	Psoas
25	chr12:56509400-56512600	Active TSS	Thymus	Thymus
26	chr12:56509400-56512600	Active TSS	NHDF-Ad	bronchial
27	chr12:56509400-56512800	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr12:56509400-56513600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:56509600-56512400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:56509600-56512400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:56509600-56512400	Active TSS	Fetal Kidney	kidney
32	chr12:56509600-56512400	Active TSS	Fetal Lung	lung
33	chr12:56509600-56512400	Active TSS	GM12878-XiMat	blood
34	chr12:56509600-56512400	Active TSS	Hela-S3	cervix
35	chr12:56509600-56512400	Active TSS	HUVEC	blood vessel
36	chr12:56509600-56512400	Active TSS	NH-A	brain
37	chr12:56509600-56512600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:56509600-56512600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:56509600-56512600	Active TSS	Esophagus	oesophagus
40	chr12:56509600-56512800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:56509600-56512800	Active TSS	Ovary	ovary
42	chr12:56509600-56512800	Active TSS	HSMMtube	muscle
43	chr12:56509800-56512400	Active TSS	Placenta Amnion	Placenta Amnion
44	chr12:56510000-56512600	Active TSS	Gastric	stomach
45	chr12:56510600-56512800	Transcr. at gene 5' and 3'	Dnd41	blood
46	chr12:56510800-56512600	Active TSS	HepG2	liver
47	chr12:56510800-56513400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr12:56511000-56513400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr12:56511200-56512400	Active TSS	Fetal Brain Male	brain
50	chr12:56511200-56512600	Active TSS	Muscle Satellite Cultured Cells	--

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