Variant report

Variant	rs13384496
Chromosome Location	chr2:231091024-231091025
allele	C/G
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	chr2:231090057-231091207	GM19193	blood:	n/a	n/a
2	POLR2A	chr2:231090065-231091288	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:231089969-231091221	GM15510	blood:	n/a	n/a
4	CHD1	chr2:231090074-231091266	GM12878	blood:	n/a	n/a
5	EBF1	chr2:231090951-231091168	GM12878	blood:	n/a	n/a
6	CEBPB	chr2:231090041-231091508	GM12878	blood:	n/a	chr2:231090430-231090441 chr2:231090431-231090442
7	EP300	chr2:231090109-231091334	GM12878	blood:	n/a	chr2:231091125-231091134 chr2:231090224-231090233 chr2:231090441-231090455 chr2:231091124-231091138 chr2:231090448-231090462
8	POLR2A	chr2:231090090-231091217	GM18951	blood:	n/a	n/a
9	POLR2A	chr2:231090968-231091207	GM12878	blood:	n/a	n/a
10	MEF2A	chr2:231090863-231091425	GM12878	blood:	n/a	chr2:231090981-231090996
11	NFIC	chr2:231090866-231091503	GM12878	blood:	n/a	n/a
12	STAT5A	chr2:231090880-231091246	GM12878	blood:	n/a	chr2:231091129-231091140
13	SPI1	chr2:231090419-231091634	GM12878	blood:	n/a	chr2:231091123-231091136 chr2:231091185-231091198 chr2:231091129-231091138
14	POLR2A	chr2:231089909-231091478	GM12878	blood:	n/a	n/a
15	SIN3A	chr2:231090109-231091192	GM12878	blood:	n/a	n/a
16	SPI1	chr2:231090852-231091433	GM12891	blood:	n/a	chr2:231091123-231091136 chr2:231091185-231091198 chr2:231091129-231091138
17	BCL11A	chr2:231090889-231091382	GM12878	blood:	n/a	chr2:231091129-231091138
18	POLR2A	chr2:231089884-231091284	GM12891	blood:	n/a	n/a
19	MAZ	chr2:231090180-231091294	GM12878	blood:	n/a	n/a
20	WRNIP1	chr2:231090083-231091070	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:231089800-231091367	GM12892	blood:	n/a	n/a
22	FOXM1	chr2:231090889-231091475	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:231090057-231091306	GM19099	blood:	n/a	n/a
24	POLR2A	chr2:231089755-231091410	GM12892	blood:	n/a	n/a
25	RUNX3	chr2:231089975-231091439	GM12878	blood:	n/a	n/a
26	POU2F2	chr2:231090917-231091163	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:231089903-231091281	Raji	blood:	n/a	n/a
28	RELA	chr2:231089827-231091287	GM15510	blood:	n/a	n/a
29	NFATC1	chr2:231090824-231091383	GM12878	blood:	n/a	n/a
30	EP300	chr2:231090946-231091328	GM12878	blood:	n/a	chr2:231091125-231091134 chr2:231091124-231091138
31	ATF2	chr2:231090116-231091431	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:231089989-231091306	GM12892	blood:	n/a	n/a
33	TAF1	chr2:231090907-231091270	GM12878	blood:	n/a	n/a
34	CHD2	chr2:231090030-231091294	GM12878	blood:	n/a	n/a
35	SPI1	chr2:231090923-231091299	HL-60	blood:	n/a	chr2:231091123-231091136 chr2:231091185-231091198 chr2:231091129-231091138
36	SPI1	chr2:231090975-231091284	GM12878	blood:	n/a	chr2:231091123-231091136 chr2:231091185-231091198 chr2:231091129-231091138
37	BCLAF1	chr2:231090853-231091408	GM12878	blood:	n/a	chr2:231091129-231091138
38	NFIC	chr2:231089779-231091691	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:231090785-231091205	GM12891	blood:	n/a	n/a
40	TBL1XR1	chr2:231090263-231091417	GM12878	blood:	n/a	n/a
41	NFATC1	chr2:231090082-231091385	GM12878	blood:	n/a	n/a
42	POLR2A	chr2:231090015-231091323	GM12892	blood:	n/a	n/a
43	TBP	chr2:231090097-231091345	GM12878	blood:	n/a	n/a
44	RELA	chr2:231090161-231091354	GM18505	blood:	n/a	n/a
45	RELA	chr2:231090228-231091337	GM19099	blood:	n/a	n/a
46	BCL11A	chr2:231090994-231091309	GM12878	blood:	n/a	chr2:231091129-231091138
47	RCOR1	chr2:231090267-231091320	GM12878	blood:	n/a	n/a
48	MTA3	chr2:231090017-231091343	GM12878	blood:	n/a	n/a
49	SPI1	chr2:231090858-231091313	HL-60	blood:	n/a	chr2:231091123-231091136 chr2:231091185-231091198 chr2:231091129-231091138
50	POLR2A	chr2:231090066-231091236	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
SP140	TF binding region
SP110	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10164566	1.00[YRI][hapmap]
rs10174828	1.00[AMR][1000 genomes]
rs10174945	1.00[AMR][1000 genomes]
rs10183659	1.00[AFR][1000 genomes]
rs10185385	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs10187268	1.00[AFR][1000 genomes]
rs10197151	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10200975	1.00[AMR][1000 genomes]
rs10208536	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs13382790	1.00[AMR][1000 genomes]
rs13392074	1.00[AFR][1000 genomes]
rs13395963	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13404885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28733458	1.00[AFR][1000 genomes]
rs4343458	1.00[YRI][hapmap]
rs6743287	1.00[AMR][1000 genomes]
rs6761254	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9653377	1.00[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	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231085000-231094800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:231085400-231092000	Weak transcription	Pancreas	Pancrea
3	chr2:231086400-231095000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:231088800-231091200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr2:231088800-231091800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:231089200-231091200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr2:231089800-231091400	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr2:231089800-231092200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:231089800-231093200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr2:231090000-231091200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:231090000-231091200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr2:231090000-231091600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr2:231090000-231092600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr2:231090200-231091200	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr2:231090200-231091800	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr2:231090200-231093800	Active TSS	Primary B cells from peripheral blood	blood
17	chr2:231090200-231170000	Weak transcription	Spleen	Spleen
18	chr2:231090400-231091200	Active TSS	Primary T cells fromperipheralblood	blood
19	chr2:231090400-231091400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr2:231090400-231091800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:231090400-231091800	Active TSS	GM12878-XiMat	blood
22	chr2:231090400-231092200	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr2:231090400-231093200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:231090400-231093200	Active TSS	Duodenum Mucosa	Duodenum
25	chr2:231090600-231091800	Weak transcription	Esophagus	oesophagus
26	chr2:231090800-231091400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:231090800-231091600	Bivalent Enhancer	HepG2	liver
28	chr2:231090800-231092200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:231090800-231092600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:231091000-231091200	Active TSS	Primary B cells from cord blood	blood
31	chr2:231091000-231091400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr2:231091000-231091800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:231091000-231092800	Weak transcription	Colonic Mucosa	Colon
34	chr2:231091000-231094800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:231091000-231102600	Weak transcription	Small Intestine	intestine

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