Variant report

Variant	rs2254475
Chromosome Location	chr12:40587055-40587056
allele	A/C
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	MAZ	chr12:40586600-40587183	GM12878	blood:	n/a	n/a
2	MEF2C	chr12:40586610-40587295	GM12878	blood:	n/a	n/a
3	CHD1	chr12:40586562-40587281	GM12878	blood:	n/a	n/a
4	SP1	chr12:40586382-40587148	GM12878	blood:	n/a	n/a
5	RELA	chr12:40586393-40587378	GM12891	blood:	n/a	n/a
6	BCL11A	chr12:40586465-40587065	GM12878	blood:	n/a	n/a
7	MEF2A	chr12:40586530-40587160	GM12878	blood:	n/a	n/a
8	EP300	chr12:40586479-40587058	GM12878	blood:	n/a	n/a
9	POU2F2	chr12:40586461-40587281	GM12878	blood:	n/a	n/a
10	FOXM1	chr12:40586404-40587183	GM12878	blood:	n/a	n/a
11	SPI1	chr12:40586462-40587125	GM12878	blood:	n/a	n/a
12	SPI1	chr12:40586450-40587129	GM12891	blood:	n/a	n/a
13	FOXM1	chr12:40586416-40587137	GM12878	blood:	n/a	n/a
14	ZNF384	chr12:40585946-40587130	GM12878	blood:	n/a	n/a
15	RELA	chr12:40586366-40587301	GM12878	blood:	n/a	n/a
16	MTA3	chr12:40586401-40587222	GM12878	blood:	n/a	n/a
17	RELA	chr12:40586253-40587360	GM18951	blood:	n/a	n/a
18	SP1	chr12:40586448-40587141	GM12878	blood:	n/a	n/a
19	PAX5	chr12:40586410-40587177	GM12878	blood:	n/a	chr12:40586893-40586912
20	EBF1	chr12:40586394-40587108	GM12878	blood:	n/a	n/a
21	PAX5	chr12:40586684-40587127	GM12892	blood:	n/a	chr12:40586893-40586912
22	RELA	chr12:40586374-40587289	GM19099	blood:	n/a	n/a
23	EP300	chr12:40586294-40587217	GM12878	blood:	n/a	n/a
24	POU2F2	chr12:40586522-40587117	GM12878	blood:	n/a	n/a
25	CUX1	chr12:40586703-40587080	GM12878	blood:	n/a	n/a
26	MEF2A	chr12:40586387-40587187	GM12878	blood:	n/a	n/a
27	RCOR1	chr12:40586329-40587132	GM12878	blood:	n/a	n/a
28	POU2F2	chr12:40586714-40587115	GM12891	blood:	n/a	n/a
29	EBF1	chr12:40586684-40587065	GM12878	blood:	n/a	n/a
30	ATF2	chr12:40586412-40587192	GM12878	blood:	n/a	n/a
31	RELA	chr12:40586442-40587486	GM19193	blood:	n/a	n/a
32	SMC3	chr12:40586884-40587141	GM12878	blood:	n/a	n/a
33	RUNX3	chr12:40586380-40587138	GM12878	blood:	n/a	n/a
34	PAX5	chr12:40586676-40587075	GM12891	blood:	n/a	chr12:40586893-40586912
35	PAX5	chr12:40586531-40587119	GM12878	blood:	n/a	chr12:40586893-40586912
36	NFIC	chr12:40586156-40587180	GM12878	blood:	n/a	n/a
37	MXI1	chr12:40586282-40587213	GM12878	blood:	n/a	n/a
38	SPI1	chr12:40586252-40587283	GM12878	blood:	n/a	n/a
39	EP300	chr12:40586482-40587248	GM12878	blood:	n/a	n/a
40	STAT3	chr12:40586543-40587070	GM12878	blood:	n/a	n/a
41	CHD2	chr12:40586158-40587275	GM12878	blood:	n/a	n/a
42	ELK1	chr12:40586548-40587139	GM12878	blood:	n/a	n/a
43	BHLHE40	chr12:40586473-40587331	GM12878	blood:	n/a	n/a
44	TBL1XR1	chr12:40586180-40587326	GM12878	blood:	n/a	n/a
45	CREB1	chr12:40586494-40587106	GM12878	blood:	n/a	n/a
46	PAX5	chr12:40586519-40587086	GM12878	blood:	n/a	chr12:40586893-40586912
47	RUNX3	chr12:40586309-40587128	GM12878	blood:	n/a	n/a
48	NFIC	chr12:40586300-40587223	GM12878	blood:	n/a	n/a
49	TBP	chr12:40586355-40587139	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRRK2	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11564134	1.00[CEU][hapmap]
rs11564136	1.00[CEU][hapmap]
rs11564154	1.00[CEU][hapmap]
rs11564163	1.00[CEU][hapmap]
rs11564174	1.00[CEU][hapmap]
rs11564186	1.00[CEU][hapmap]
rs11564188	1.00[CEU][hapmap]
rs11564208	1.00[CEU][hapmap]
rs17519173	1.00[CEU][hapmap]
rs17519258	1.00[AMR][1000 genomes]
rs17519531	1.00[CEU][hapmap]
rs17519580	1.00[CEU][hapmap]
rs28365208	1.00[CEU][hapmap]
rs7315719	1.00[CEU][hapmap]
rs7315853	1.00[CEU][hapmap]
rs7316047	1.00[CEU][hapmap]
rs7974320	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40585600-40587200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr12:40585800-40587200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr12:40585800-40587400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr12:40586000-40587400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr12:40586000-40587600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr12:40586000-40591000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:40586200-40587200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr12:40586200-40591600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:40586400-40587200	Enhancers	HUVEC	blood vessel
10	chr12:40586600-40587200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:40586800-40587200	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr12:40586800-40587200	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr12:40586800-40588800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:40587000-40587400	Flanking Active TSS	GM12878-XiMat	blood
15	chr12:40587000-40587800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr12:40587000-40588000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:40587000-40588200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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