Variant report

Variant	rs11676418
Chromosome Location	chr2:231447589-231447590
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	ATF2	chr2:231447466-231448294	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:231447478-231449216	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:231447503-231448186	GM12891	blood:	n/a	n/a
4	FOXM1	chr2:231447041-231448305	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:231447455-231449128	GM12892	blood:	n/a	n/a
6	MTA3	chr2:231447140-231448977	GM12878	blood:	n/a	n/a
7	CHD1	chr2:231447550-231448627	GM12878	blood:	n/a	n/a
8	PML	chr2:231447286-231449090	GM12878	blood:	n/a	chr2:231448813-231448821
9	EP300	chr2:231447549-231448078	GM12878	blood:	n/a	chr2:231447804-231447818
10	BCL3	chr2:231447555-231448071	GM12878	blood:	n/a	chr2:231447804-231447813
11	POU2F2	chr2:231447587-231448162	GM12878	blood:	n/a	chr2:231447906-231447920 chr2:231447908-231447921 chr2:231447908-231447921
12	BCLAF1	chr2:231447303-231448937	GM12878	blood:	n/a	chr2:231448477-231448486 chr2:231447804-231447813 chr2:231448763-231448772
13	YY1	chr2:231447533-231448213	GM12891	blood:	n/a	n/a
14	STAT5A	chr2:231447432-231448811	GM12878	blood:	n/a	chr2:231448358-231448366 chr2:231447822-231447830 chr2:231447802-231447813
15	NFATC1	chr2:231447359-231448688	GM12878	blood:	n/a	n/a
16	MEF2A	chr2:231447550-231448079	GM12878	blood:	n/a	chr2:231447775-231447786 chr2:231447831-231447846 chr2:231447773-231447788 chr2:231447831-231447846 chr2:231447775-231447790
17	MEF2A	chr2:231447416-231448141	GM12878	blood:	n/a	chr2:231447775-231447786 chr2:231447831-231447846 chr2:231447773-231447788 chr2:231447831-231447846 chr2:231447775-231447790
18	YY1	chr2:231447507-231447866	SK-N-SH	brain:	n/a	n/a
19	NFATC1	chr2:231447384-231448213	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:231447291-231449074	GM12878	blood:	n/a	n/a
21	RCOR1	chr2:231447120-231447949	GM12878	blood:	n/a	n/a
22	EP300	chr2:231447554-231448102	GM12878	blood:	n/a	chr2:231447804-231447818
23	SPI1	chr2:231447582-231448002	GM12891	blood:	n/a	chr2:231447804-231447813
24	YY1	chr2:231447527-231448087	GM12892	blood:	n/a	n/a
25	RUNX3	chr2:231447405-231448926	GM12878	blood:	n/a	n/a
26	IKZF1	chr2:231447588-231448862	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:231447492-231449219	GM12891	blood:	n/a	n/a
28	RUNX3	chr2:231447421-231448746	GM12878	blood:	n/a	n/a
29	CREB1	chr2:231447396-231448790	GM12878	blood:	n/a	n/a
30	NFIC	chr2:231447287-231449123	GM12878	blood:	n/a	n/a
31	STAT3	chr2:231447475-231448649	GM12878	blood:	n/a	chr2:231448358-231448366 chr2:231447822-231447830 chr2:231447802-231447813
32	CEBPB	chr2:231447055-231448245	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:231447486-231448114	GM12891	blood:	n/a	n/a
34	YY1	chr2:231447534-231448147	GM12892	blood:	n/a	n/a
35	EP300	chr2:231447421-231448100	GM12878	blood:	n/a	chr2:231447804-231447818
36	YY1	chr2:231447560-231448069	K562	blood:	n/a	n/a
37	RELA	chr2:231447543-231448953	GM12891	blood:	n/a	n/a
38	POU2F2	chr2:231447586-231448143	GM12891	blood:	n/a	chr2:231447906-231447920 chr2:231447908-231447921 chr2:231447908-231447921
39	TCF12	chr2:231447579-231448126	SK-N-SH	brain:	n/a	n/a
40	GATA3	chr2:231447356-231448010	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr2:231447395-231449112	GM12892	blood:	n/a	n/a
42	BCL11A	chr2:231447562-231448097	GM12878	blood:	n/a	chr2:231447804-231447813
43	SPI1	chr2:231447555-231448099	GM12891	blood:	n/a	chr2:231447804-231447813
44	YY1	chr2:231447498-231448143	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:231447579-231449114	GM12878	blood:	n/a	n/a
46	POLR2A	chr2:231447457-231448174	GM12892	blood:	n/a	n/a
47	MTA3	chr2:231447047-231449191	GM12878	blood:	n/a	n/a
48	PAX5	chr2:231447537-231448195	GM12878	blood:	n/a	n/a
49	BCLAF1	chr2:231447458-231448132	GM12878	blood:	n/a	chr2:231447804-231447813
50	ZNF143	chr2:231447581-231448080	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-451P	TF binding region
ENSG00000235419	TF binding region

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11674767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11681649	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11682332	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682484	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11686286	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11687550	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11689413	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11691070	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11692958	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11694266	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11694317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12612121	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12617821	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2241534	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2241536	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2241537	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56199999	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56289241	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73992446	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73992447	0.90[AMR][1000 genomes];0.98[EUR][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	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
2	nsv875953	chr2:231415189-231457819	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv875955	chr2:231440555-231500805	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv961010	chr2:231446732-231451285	Flanking Active TSS Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231443400-231451000	Weak transcription	Primary T cells from cord blood	blood
2	chr2:231443400-231453800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:231443400-231454400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr2:231443400-231454600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:231443800-231447600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr2:231444000-231447600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:231446800-231449000	Enhancers	Primary B cells from peripheral blood	blood
8	chr2:231447200-231448200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:231447200-231448600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:231447200-231449000	Flanking Active TSS	GM12878-XiMat	blood
11	chr2:231447400-231447600	Enhancers	Primary B cells from cord blood	blood
12	chr2:231447400-231448400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:231447400-231448400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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