Variant report

Variant	rs1561475
Chromosome Location	chr2:111873698-111873699
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	ATF2	chr2:111873498-111874121	GM12878	blood:	n/a	n/a
2	CTCF	chr2:111873049-111875558	A549	lung:	n/a	chr2:111875132-111875153 chr2:111874765-111874786 chr2:111875130-111875148 chr2:111873712-111873728 chr2:111875135-111875143
3	CTCF	chr2:111873640-111873790	Caco-2	colon:	n/a	chr2:111873712-111873728
4	RUNX3	chr2:111873408-111874352	GM12878	blood:	n/a	n/a
5	CTCF	chr2:111873584-111873880	K562	blood:	n/a	chr2:111873712-111873728
6	BCLAF1	chr2:111873517-111873948	GM12878	blood:	n/a	n/a
7	CTCF	chr2:111873647-111873779	GM12878	blood:	n/a	chr2:111873712-111873728
8	BCL3	chr2:111873469-111874018	GM12878	blood:	n/a	n/a
9	MEF2C	chr2:111873494-111874093	GM12878	blood:	n/a	chr2:111873821-111873836
10	MYC	chr2:111873546-111873746	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr2:111873676-111873772	GM13977	blood:	n/a	chr2:111873712-111873728
12	MAZ	chr2:111873371-111874331	GM12878	blood:	n/a	n/a
13	ZNF384	chr2:111873510-111874302	GM12878	blood:	n/a	n/a
14	IRF4	chr2:111873463-111874259	GM12878	blood:	n/a	n/a
15	RAD21	chr2:111873529-111873794	GM12878	blood:	n/a	n/a
16	PAX5	chr2:111873573-111873927	GM12878	blood:	n/a	n/a
17	SP1	chr2:111873527-111874204	GM12878	blood:	n/a	n/a
18	STAT5A	chr2:111873440-111874110	GM12878	blood:	n/a	n/a
19	BCL11A	chr2:111873498-111874315	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:111873598-111873865	GM12878	blood:	n/a	n/a
21	RELA	chr2:111873521-111874192	GM19099	blood:	n/a	n/a
22	BCLAF1	chr2:111873461-111874247	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr2:111873466-111875169	GM12878	blood:	n/a	n/a
24	PBX3	chr2:111873663-111873859	GM12878	blood:	n/a	n/a
25	MXI1	chr2:111873483-111874911	GM12878	blood:	n/a	n/a
26	SMC3	chr2:111873459-111875292	GM12878	blood:	n/a	chr2:111874765-111874779
27	POU2F2	chr2:111873567-111873974	GM12878	blood:	n/a	chr2:111873678-111873691 chr2:111873668-111873681 chr2:111873666-111873680 chr2:111873668-111873681 chr2:111873668-111873681
28	MEF2A	chr2:111873394-111874096	GM12878	blood:	n/a	chr2:111873821-111873836
29	SP1	chr2:111873589-111873940	GM12878	blood:	n/a	n/a
30	STAT1	chr2:111873580-111874175	GM12878	blood:	n/a	n/a
31	IKZF1	chr2:111873367-111874812	GM12878	blood:	n/a	n/a
32	EP300	chr2:111873495-111873989	GM12878	blood:	n/a	n/a
33	CTCF	chr2:111873338-111875311	GM12878	blood:	n/a	chr2:111875132-111875153 chr2:111874765-111874786 chr2:111875130-111875148 chr2:111873712-111873728 chr2:111875135-111875143
34	BATF	chr2:111873546-111874273	GM12878	blood:	n/a	n/a
35	RAD21	chr2:111873500-111875165	GM12878	blood:	n/a	chr2:111874765-111874779 chr2:111875131-111875150 chr2:111874764-111874783 chr2:111874715-111874722
36	FOXM1	chr2:111873441-111874300	GM12878	blood:	n/a	n/a
37	CTCF	chr2:111873640-111873790	HMEC	breast:	n/a	chr2:111873712-111873728
38	POU2F2	chr2:111873468-111874274	GM12878	blood:	n/a	chr2:111873678-111873691 chr2:111873668-111873681 chr2:111873666-111873680 chr2:111873668-111873681 chr2:111873668-111873681
39	MTA3	chr2:111873491-111874075	GM12878	blood:	n/a	n/a
40	CEBPB	chr2:111873639-111873910	GM12878	blood:	n/a	chr2:111873688-111873700
41	RUNX3	chr2:111873372-111874425	GM12878	blood:	n/a	n/a
42	RELA	chr2:111873407-111874460	GM12878	blood:	n/a	n/a
43	PAX5	chr2:111873472-111874294	GM12878	blood:	n/a	n/a
44	CTCF	chr2:111873680-111873787	GM10248	blood:	n/a	chr2:111873712-111873728
45	TBP	chr2:111873617-111874018	GM12878	blood:	n/a	n/a
46	CUX1	chr2:111873535-111874354	GM12878	blood:	n/a	n/a
47	PML	chr2:111873403-111874220	GM12878	blood:	n/a	n/a
48	EP300	chr2:111873445-111874964	GM12878	blood:	n/a	n/a
49	ZNF143	chr2:111873526-111874074	GM12878	blood:	n/a	n/a
50	ELK1	chr2:111873599-111874103	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111807803..111810295-chr2:111873286..111875323,2	MCF-7	breast:
2	chr2:111786376..111787035-chr2:111873340..111875017,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204581	TF binding region
BCL2L11	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6759769	1.00[YRI][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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv874842	chr2:111870220-111892984	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111860200-111875000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:111867000-111874400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:111869000-111874600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:111873000-111874000	Enhancers	Fetal Intestine Small	intestine
5	chr2:111873400-111874400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:111873400-111874400	Bivalent Enhancer	GM12878-XiMat	blood

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