Variant report

Variant	rs11115342
Chromosome Location	chr12:83076731-83076732
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	FOS	chr12:83076620-83076905	MCF10A-Er-Src	breast:	n/a	chr12:83076659-83076671
2	CEBPB	chr12:83076411-83077058	MCF-7	breast:	n/a	chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076769-83076782 chr12:83076771-83076782 chr12:83076769-83076782 chr12:83076771-83076780 chr12:83076769-83076780
3	SIN3AK20	chr12:83076307-83077293	MCF-7	breast:	n/a	n/a
4	CEBPB	chr12:83076579-83077151	A549	lung:	n/a	chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076769-83076782 chr12:83076771-83076782 chr12:83076769-83076782 chr12:83076771-83076780 chr12:83076769-83076780
5	SP1	chr12:83076500-83076993	A549	lung:	n/a	n/a
6	GATA3	chr12:83076584-83076861	MCF-7	breast:	n/a	n/a
7	EP300	chr12:83076386-83076987	T-47D	breast:	n/a	chr12:83076770-83076784 chr12:83076907-83076916
8	MXI1	chr12:83075860-83076920	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr12:83076186-83077174	A549	lung:	n/a	n/a
10	FOS	chr12:83076650-83076904	MCF10A-Er-Src	breast:	n/a	chr12:83076659-83076671
11	SP1	chr12:83076467-83077069	A549	lung:	n/a	n/a
12	REST	chr12:83076473-83076976	A549	lung:	n/a	n/a
13	GATA3	chr12:83076403-83077031	T-47D	breast:	n/a	n/a
14	GATA3	chr12:83076509-83076999	MCF-7	breast:	n/a	n/a
15	STAT3	chr12:83076686-83076907	MCF10A-Er-Src	breast:	n/a	chr12:83076771-83076779
16	GATA3	chr12:83076274-83077112	MCF-7	breast:	n/a	n/a
17	MYC	chr12:83076606-83077082	MCF10A-Er-Src	breast:	n/a	n/a
18	FOXA2	chr12:83076491-83077011	A549	lung:	n/a	n/a
19	JUND	chr12:83076438-83077146	T-47D	breast:	n/a	chr12:83076659-83076671 chr12:83077030-83077039
20	NR2F2	chr12:83076450-83077126	MCF-7	breast:	n/a	n/a
21	POLR2A	chr12:83076523-83076989	SK-N-MC	brain:	n/a	n/a
22	SPI1	chr12:83076712-83077016	HL-60	blood:	n/a	chr12:83076917-83076930
23	EP300	chr12:83076464-83076958	T-47D	breast:	n/a	chr12:83076770-83076784 chr12:83076907-83076916
24	CEBPB	chr12:83076582-83077071	Hela-S3	cervix:	n/a	chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076769-83076782 chr12:83076771-83076782 chr12:83076769-83076782 chr12:83076771-83076780 chr12:83076769-83076780
25	TCF7L2	chr12:83076425-83076990	MCF-7	breast:	n/a	chr12:83076850-83076866 chr12:83076669-83076683
26	EP300	chr12:83076593-83076915	Hela-S3	cervix:	n/a	chr12:83076770-83076784
27	SIN3AK20	chr12:83076401-83077163	MCF-7	breast:	n/a	n/a
28	FOXA1	chr12:83076348-83077074	T-47D	breast:	n/a	chr12:83076794-83076809
29	EP300	chr12:83076502-83076985	A549	lung:	n/a	chr12:83076770-83076784 chr12:83076907-83076916
30	CEBPB	chr12:83076584-83076969	HepG2	liver:	n/a	chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076769-83076782 chr12:83076771-83076782 chr12:83076769-83076782 chr12:83076771-83076780 chr12:83076769-83076780
31	FOS	chr12:83076647-83077005	MCF10A-Er-Src	breast:	n/a	chr12:83076659-83076671
32	JUND	chr12:83076374-83077167	T-47D	breast:	n/a	chr12:83076659-83076671 chr12:83077030-83077039
33	CEBPB	chr12:83076594-83076965	IMR90	lung:	n/a	chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076769-83076782 chr12:83076771-83076782 chr12:83076769-83076782 chr12:83076771-83076780 chr12:83076769-83076780
34	GATA3	chr12:83076406-83077047	MCF-7	breast:	n/a	n/a
35	CEBPB	chr12:83076607-83077026	A549	lung:	n/a	chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076769-83076782 chr12:83076771-83076782 chr12:83076769-83076782 chr12:83076771-83076780 chr12:83076769-83076780
36	STAT3	chr12:83076651-83076972	MCF10A-Er-Src	breast:	n/a	chr12:83076771-83076779
37	CEBPB	chr12:83076599-83076918	K562	blood:	n/a	chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076769-83076782 chr12:83076771-83076782 chr12:83076769-83076782 chr12:83076771-83076780 chr12:83076769-83076780
38	SPI1	chr12:83076599-83077152	HL-60	blood:	n/a	chr12:83076917-83076930
39	HDAC2	chr12:83076493-83076990	MCF-7	breast:	n/a	n/a
40	GATA3	chr12:83076392-83077105	T-47D	breast:	n/a	n/a
41	FOXA1	chr12:83076469-83077091	T-47D	breast:	n/a	chr12:83076794-83076809
42	NR2F2	chr12:83076549-83077119	MCF-7	breast:	n/a	n/a
43	GATA3	chr12:83076496-83077020	A549	lung:	n/a	n/a
44	HDAC2	chr12:83076425-83077071	MCF-7	breast:	n/a	n/a
45	POLR2A	chr12:83076701-83076901	MCF10A-Er-Src	breast:	n/a	n/a
46	CEBPB	chr12:83076458-83077066	A549	lung:	n/a	chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076769-83076782 chr12:83076771-83076782 chr12:83076769-83076782 chr12:83076771-83076780 chr12:83076769-83076780
47	ZNF217	chr12:83076574-83077034	MCF-7	breast:	n/a	n/a
48	CEBPB	chr12:83076608-83076934	H1-hESC	embryonic stem cell:	n/a	chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076771-83076780 chr12:83076769-83076782 chr12:83076771-83076782 chr12:83076769-83076782 chr12:83076771-83076780 chr12:83076769-83076780
49	FOXA2	chr12:83076557-83077009	A549	lung:	n/a	n/a
50	MYC	chr12:83076580-83077004	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:83072653..83078667-chr12:83078860..83082223,14	MCF-7	breast:
2	chr12:83075987..83078783-chr12:83079698..83081470,2	K562	blood:
3	chr12:83068566..83070465-chr12:83075258..83077801,3	MCF-7	breast:

Variant related genes	Relation type
TMTC2	TF binding region
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10862497	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11115339	0.86[AMR][1000 genomes]
rs11115348	1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11115353	0.88[EUR][1000 genomes]
rs11115355	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11609532	0.92[EUR][1000 genomes]
rs11610988	0.80[EUR][1000 genomes]
rs11613168	0.80[EUR][1000 genomes]
rs11614435	0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs11615763	0.80[EUR][1000 genomes]
rs11615765	0.80[EUR][1000 genomes]
rs12305736	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12307168	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12422405	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12423043	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12426166	0.94[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13377925	0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17009812	0.84[EUR][1000 genomes]
rs17009851	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009854	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17009856	1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009882	0.82[EUR][1000 genomes]
rs17009885	0.82[EUR][1000 genomes]
rs17009891	0.80[EUR][1000 genomes]
rs17009893	0.80[EUR][1000 genomes]
rs17009899	0.80[EUR][1000 genomes]
rs1922576	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1922579	0.91[EUR][1000 genomes]
rs4620789	0.94[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4882428	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55657485	0.92[EUR][1000 genomes]
rs56298822	0.95[EUR][1000 genomes]
rs56396658	0.92[EUR][1000 genomes]
rs61485473	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6539683	0.81[EUR][1000 genomes]
rs7134747	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7134766	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7135486	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72615654	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7294890	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7303469	0.84[EUR][1000 genomes]
rs7306509	0.80[YRI][hapmap]
rs7313778	0.87[EUR][1000 genomes]
rs73354481	0.84[EUR][1000 genomes]
rs74106267	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7954021	0.86[AMR][1000 genomes]
rs7961953	1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7975647	1.00[CEU][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9805078	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv899349	chr12:82931646-83114286	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83075600-83076800	Enhancers	Brain Cingulate Gyrus	brain
2	chr12:83075800-83076800	Enhancers	Fetal Kidney	kidney
3	chr12:83075800-83077000	Enhancers	Brain Germinal Matrix	brain
4	chr12:83075800-83077200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr12:83075800-83077200	Enhancers	Fetal Lung	lung
6	chr12:83075800-83077600	Enhancers	Fetal Stomach	stomach
7	chr12:83075800-83079600	Enhancers	Stomach Mucosa	stomach
8	chr12:83076000-83076800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:83076000-83076800	Enhancers	Brain Substantia Nigra	brain
10	chr12:83076000-83077000	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:83076000-83077000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr12:83076000-83077000	Enhancers	Brain Anterior Caudate	brain
13	chr12:83076000-83077000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr12:83076000-83077000	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr12:83076000-83077200	Enhancers	Adipose Nuclei	Adipose
16	chr12:83076000-83077200	Enhancers	Colon Smooth Muscle	Colon
17	chr12:83076200-83076800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:83076200-83076800	Enhancers	A549	lung
19	chr12:83076200-83077000	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr12:83076200-83077000	Enhancers	Fetal Brain Female	brain
21	chr12:83076200-83077000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr12:83076200-83077000	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:83076200-83077000	Enhancers	Stomach Smooth Muscle	stomach
24	chr12:83076200-83077200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:83076200-83077400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr12:83076200-83077400	Enhancers	Hela-S3	cervix
27	chr12:83076200-83077600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr12:83076200-83079400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr12:83076200-83079600	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr12:83076400-83077000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr12:83076600-83076800	Enhancers	Fetal Heart	heart
32	chr12:83076600-83077000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:83076600-83077000	Enhancers	GM12878-XiMat	blood
34	chr12:83076600-83079600	Weak transcription	H1 Cell Line	embryonic stem cell

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