Variant report

Variant	rs11063002
Chromosome Location	chr12:4228251-4228252
allele	A/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	IRF4	chr12:4227090-4228928	GM12878	blood:	n/a	n/a
2	BHLHE40	chr12:4226533-4228890	GM12878	blood:	n/a	chr12:4227505-4227526
3	EP300	chr12:4228114-4228916	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr12:4227005-4228962	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:4223920-4228953	GM12878	blood:	n/a	n/a
6	RELA	chr12:4225873-4228933	GM19099	blood:	n/a	chr12:4226252-4226261 chr12:4226252-4226261
7	IRF4	chr12:4227870-4229011	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:4225411-4228750	GM18526	blood:	n/a	n/a
9	POLR2A	chr12:4227611-4228447	GM12891	blood:	n/a	n/a
10	EBF1	chr12:4228207-4228840	GM12878	blood:	n/a	n/a
11	CUX1	chr12:4228124-4228732	GM12878	blood:	n/a	n/a
12	CHD1	chr12:4226563-4229101	GM12878	blood:	n/a	n/a
13	ATF2	chr12:4228012-4228940	GM12878	blood:	n/a	n/a
14	BCL3	chr12:4228121-4228887	GM12878	blood:	n/a	n/a
15	MAZ	chr12:4226875-4228730	GM12878	blood:	n/a	chr12:4227961-4227971
16	NFIC	chr12:4228083-4228928	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:4226356-4228594	GM15510	blood:	n/a	n/a
18	ATF2	chr12:4227986-4228978	GM12878	blood:	n/a	n/a
19	RELA	chr12:4228228-4228852	GM12892	blood:	n/a	n/a
20	CEBPB	chr12:4228152-4229019	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:4224737-4228840	GM19099	blood:	n/a	n/a
22	BCL11A	chr12:4228233-4228820	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:4227049-4228811	GM12891	blood:	n/a	n/a
24	POLR2A	chr12:4225264-4228852	GM12891	blood:	n/a	n/a
25	YY1	chr12:4227673-4228425	GM12892	blood:	n/a	n/a
26	POLR2A	chr12:4226646-4228749	GM12892	blood:	n/a	n/a
27	POLR2A	chr12:4227631-4228414	GM12891	blood:	n/a	n/a
28	SP1	chr12:4228102-4228877	GM12878	blood:	n/a	n/a
29	NFATC1	chr12:4228116-4229050	GM12878	blood:	n/a	n/a
30	TAF1	chr12:4228186-4228530	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:4225332-4228715	GM12878	blood:	n/a	n/a
32	MXI1	chr12:4226316-4228818	GM12878	blood:	n/a	n/a
33	RELA	chr12:4227022-4228862	GM18526	blood:	n/a	n/a
34	POLR2A	chr12:4227927-4228276	GM12878	blood:	n/a	n/a
35	EBF1	chr12:4226490-4228903	GM12878	blood:	n/a	chr12:4226955-4226964 chr12:4226954-4226965 chr12:4227037-4227047 chr12:4226953-4226966 chr12:4227036-4227047 chr12:4227038-4227047
36	POU2F2	chr12:4227000-4228761	GM12891	blood:	n/a	chr12:4227885-4227897
37	EP300	chr12:4228118-4228810	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:4227030-4228714	GM12892	blood:	n/a	n/a
39	ZNF143	chr12:4228073-4228965	GM12878	blood:	n/a	n/a
40	TCF3	chr12:4228229-4228784	GM12878	blood:	n/a	chr12:4228447-4228460
41	POLR2A	chr12:4224082-4228709	GM19193	blood:	n/a	n/a
42	PAX5	chr12:4228125-4228703	GM12878	blood:	n/a	n/a
43	RELA	chr12:4226556-4228923	GM10847	blood:	n/a	n/a
44	BATF	chr12:4228185-4228976	GM12878	blood:	n/a	n/a
45	RELA	chr12:4226143-4228935	GM12878	blood:	n/a	chr12:4226252-4226261 chr12:4226252-4226261
46	NFIC	chr12:4227964-4229016	GM12878	blood:	n/a	n/a
47	SP1	chr12:4227157-4228800	GM12878	blood:	n/a	n/a
48	MEF2A	chr12:4228177-4228780	GM12878	blood:	n/a	n/a
49	RELA	chr12:4226135-4228945	GM12891	blood:	n/a	chr12:4226252-4226261 chr12:4226252-4226261
50	STAT3	chr12:4228166-4228916	GM12878	blood:	n/a	chr12:4228299-4228310

Variant related genes	Relation type
ENSG00000242444	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10459129	0.91[ASN][1000 genomes]
rs10744631	0.91[ASN][1000 genomes]
rs10774193	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10774197	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848978	0.83[EUR][1000 genomes]
rs10848979	0.85[EUR][1000 genomes]
rs10848981	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848982	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848983	0.86[EUR][1000 genomes]
rs10848984	0.85[EUR][1000 genomes]
rs10848985	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11062999	0.82[EUR][1000 genomes]
rs11063000	0.82[EUR][1000 genomes]
rs11063003	1.00[EUR][1000 genomes]
rs11063004	0.86[EUR][1000 genomes]
rs11063007	0.86[EUR][1000 genomes]
rs11063008	0.87[EUR][1000 genomes]
rs11063009	0.88[EUR][1000 genomes]
rs11063011	0.91[ASN][1000 genomes]
rs11063012	0.91[ASN][1000 genomes]
rs12228949	0.83[EUR][1000 genomes]
rs12229320	0.88[EUR][1000 genomes]
rs12230013	0.83[EUR][1000 genomes]
rs12579541	0.88[EUR][1000 genomes]
rs12579556	0.88[EUR][1000 genomes]
rs12579813	0.88[EUR][1000 genomes]
rs2003578	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003579	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098332	0.81[EUR][1000 genomes]
rs2110592	0.88[EUR][1000 genomes]
rs2160160	0.87[EUR][1000 genomes]
rs2160161	0.88[EUR][1000 genomes]
rs2247533	0.83[EUR][1000 genomes]
rs2358593	0.83[EUR][1000 genomes]
rs2358836	0.88[EUR][1000 genomes]
rs2358837	0.88[EUR][1000 genomes]
rs2724204	0.85[EUR][1000 genomes]
rs3889565	0.82[EUR][1000 genomes]
rs4765769	0.83[EUR][1000 genomes]
rs4766207	0.88[EUR][1000 genomes]
rs4766208	0.87[EUR][1000 genomes]
rs4766209	0.88[EUR][1000 genomes]
rs4766211	0.88[EUR][1000 genomes]
rs58334161	0.88[EUR][1000 genomes]
rs60789908	0.83[EUR][1000 genomes]
rs6489518	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6489519	0.93[ASN][1000 genomes]
rs7136346	0.88[EUR][1000 genomes]
rs741244	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs741245	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs759306	0.86[EUR][1000 genomes]
rs759312	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7967520	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969060	0.83[EUR][1000 genomes]
rs873613	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634153	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1050474	chr12:4226760-4389238	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4224000-4228800	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr12:4224000-4229000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:4224000-4229000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:4224200-4228800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:4224200-4228800	Enhancers	Fetal Thymus	thymus
6	chr12:4224200-4230000	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:4224600-4229000	Flanking Active TSS	GM12878-XiMat	blood
8	chr12:4225600-4228800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr12:4226000-4228600	Enhancers	Small Intestine	intestine
10	chr12:4226400-4230800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:4226600-4228600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr12:4227000-4228400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr12:4227000-4229000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:4227200-4252000	Weak transcription	Pancreas	Pancrea
15	chr12:4227400-4228400	Enhancers	Colonic Mucosa	Colon
16	chr12:4227400-4231000	Enhancers	Fetal Muscle Trunk	muscle
17	chr12:4227600-4228400	Enhancers	NH-A	brain
18	chr12:4227600-4228800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr12:4227600-4229600	Enhancers	HSMMtube	muscle
20	chr12:4227600-4230200	Enhancers	HSMM	muscle
21	chr12:4227800-4228400	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr12:4227800-4228600	Enhancers	Duodenum Mucosa	Duodenum
23	chr12:4227800-4228600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr12:4227800-4229000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr12:4227800-4229200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr12:4227800-4229600	Enhancers	Primary B cells from cord blood	blood
27	chr12:4227800-4231200	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:4228000-4228600	Enhancers	Primary T cells from cord blood	blood
29	chr12:4228000-4228600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:4228000-4228800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr12:4228000-4228800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr12:4228000-4228800	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr12:4228000-4228800	Weak transcription	Right Atrium	heart
34	chr12:4228000-4231400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr12:4228000-4231400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:4228200-4228400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
37	chr12:4228200-4228400	Enhancers	Esophagus	oesophagus
38	chr12:4228200-4228600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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