Variant report

Variant	rs2276737
Chromosome Location	chr3:133167363-133167364
allele	A/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	YY1	chr3:133166790-133168007	GM12878	blood:	n/a	n/a
2	MEF2A	chr3:133167091-133167918	GM12878	blood:	n/a	n/a
3	RCOR1	chr3:133166769-133168334	GM12878	blood:	n/a	n/a
4	MTA3	chr3:133166557-133168260	GM12878	blood:	n/a	n/a
5	PML	chr3:133167283-133167744	GM12878	blood:	n/a	n/a
6	RUNX3	chr3:133167202-133168012	GM12878	blood:	n/a	n/a
7	BATF	chr3:133167292-133167760	GM12878	blood:	n/a	n/a
8	BCLAF1	chr3:133167158-133167928	GM12878	blood:	n/a	n/a
9	EBF1	chr3:133166517-133168232	GM12878	blood:	n/a	chr3:133167072-133167081 chr3:133166746-133166757
10	POU2F2	chr3:133167197-133167689	GM12878	blood:	n/a	chr3:133167305-133167313 chr3:133167303-133167314 chr3:133167300-133167318 chr3:133167304-133167316 chr3:133167303-133167314 chr3:133167302-133167317 chr3:133167304-133167319 chr3:133167304-133167314
11	ELF1	chr3:133167246-133167816	GM12878	blood:	n/a	n/a
12	CREB1	chr3:133167261-133167945	GM12878	blood:	n/a	n/a
13	CHD2	chr3:133167186-133168263	GM12878	blood:	n/a	n/a
14	STAT5A	chr3:133166923-133167832	GM12878	blood:	n/a	n/a
15	ATF2	chr3:133167079-133168028	GM12878	blood:	n/a	n/a
16	NFIC	chr3:133166502-133168337	GM12878	blood:	n/a	n/a
17	STAT5A	chr3:133167130-133168217	GM12878	blood:	n/a	n/a
18	BCLAF1	chr3:133167280-133167988	GM12878	blood:	n/a	n/a
19	RELA	chr3:133166415-133168065	GM15510	blood:	n/a	n/a
20	BCL3	chr3:133167225-133167767	GM12878	blood:	n/a	n/a
21	IKZF1	chr3:133167306-133168112	GM12878	blood:	n/a	n/a
22	BHLHE40	chr3:133166690-133168104	GM12878	blood:	n/a	n/a
23	TBP	chr3:133167161-133168194	GM12878	blood:	n/a	n/a
24	CUX1	chr3:133167108-133168109	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:133166633-133168087	Raji	blood:	n/a	n/a
26	EBF1	chr3:133167338-133167909	GM12878	blood:	n/a	n/a
27	MEF2C	chr3:133167149-133167888	GM12878	blood:	n/a	n/a
28	SMC3	chr3:133167102-133168017	GM12878	blood:	n/a	n/a
29	BCL11A	chr3:133167273-133167755	GM12878	blood:	n/a	n/a
30	EP300	chr3:133167221-133168206	GM12878	blood:	n/a	n/a
31	MXI1	chr3:133167083-133168120	GM12878	blood:	n/a	n/a
32	NFATC1	chr3:133167012-133167950	GM12878	blood:	n/a	n/a
33	SRF	chr3:133167301-133167611	GM12878	blood:	n/a	n/a
34	SP1	chr3:133167284-133167953	GM12878	blood:	n/a	chr3:133167492-133167506
35	ESR1	chr3:133167350-133168085	T-47D	breast:	n/a	n/a
36	RUNX3	chr3:133166585-133168260	GM12878	blood:	n/a	n/a
37	PAX5	chr3:133167194-133167887	GM12878	blood:	n/a	n/a
38	RELA	chr3:133166562-133168217	GM19193	blood:	n/a	n/a
39	RELA	chr3:133166619-133168123	GM18951	blood:	n/a	n/a
40	POLR2A	chr3:133167285-133168264	GM12878	blood:	n/a	n/a
41	EP300	chr3:133167258-133167780	GM12878	blood:	n/a	n/a
42	YY1	chr3:133167184-133167691	K562	blood:	n/a	n/a
43	EP300	chr3:133166771-133168225	GM12878	blood:	n/a	n/a
44	IRF4	chr3:133167174-133167908	GM12878	blood:	n/a	n/a
45	ATF2	chr3:133166990-133168141	GM12878	blood:	n/a	n/a
46	POU2F2	chr3:133167163-133167788	GM12891	blood:	n/a	chr3:133167305-133167313 chr3:133167303-133167314 chr3:133167300-133167318 chr3:133167304-133167316 chr3:133167303-133167314 chr3:133167302-133167317 chr3:133167304-133167319 chr3:133167304-133167314
47	PML	chr3:133166461-133168247	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:133167323-133167785	GM12891	blood:	n/a	n/a
49	POU2F2	chr3:133167187-133167792	GM12878	blood:	n/a	chr3:133167305-133167313 chr3:133167303-133167314 chr3:133167300-133167318 chr3:133167304-133167316 chr3:133167303-133167314 chr3:133167302-133167317 chr3:133167304-133167319 chr3:133167304-133167314
50	PAX5	chr3:133167328-133167823	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:133167229..133167755-chr3:133175434..133175991,2	MCF-7	breast:
2	chr3:133165936..133167701-chr3:133170915..133173583,2	MCF-7	breast:
3	chr3:133164640..133168534-chr3:133291750..133294077,5	MCF-7	breast:

Variant related genes	Relation type
BFSP2	TF binding region
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10935064	0.81[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11715830	0.85[ASN][1000 genomes]
rs13069027	0.81[JPT][hapmap]
rs1881918	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2078262	0.86[JPT][hapmap]
rs2737717	0.81[CHB][hapmap]
rs2859679	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7612063	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs931099	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9808983	0.83[ASN][1000 genomes]
rs9883661	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877504	chr3:133122216-133172374	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv522281	chr3:133137434-133167363	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1007047	chr3:133137664-133181388	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1006289	chr3:133137664-133186808	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1829199	chr3:133158065-133213047	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv877505	chr3:133167363-133235272	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2276737	SOX14	cis	cerebellum	SCAN
rs2276737	TF	cis	parietal	SCAN
rs2276737	ESYT3	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133161000-133168000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:133161000-133191000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:133161600-133167800	Weak transcription	Primary T cells from cord blood	blood
4	chr3:133162400-133170400	Enhancers	Fetal Thymus	thymus
5	chr3:133163200-133167400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:133163200-133167600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:133163400-133167600	Weak transcription	HepG2	liver
8	chr3:133163800-133169200	Weak transcription	Pancreas	Pancrea
9	chr3:133164200-133167400	Weak transcription	Placenta	Placenta
10	chr3:133165400-133178600	Weak transcription	Aorta	Aorta
11	chr3:133165600-133170400	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:133166000-133168200	Enhancers	Brain Germinal Matrix	brain
13	chr3:133166000-133168200	Enhancers	Fetal Kidney	kidney
14	chr3:133166000-133169400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:133166200-133169000	Enhancers	Primary B cells from cord blood	blood
16	chr3:133166200-133169200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr3:133166200-133169400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:133166400-133167800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:133166400-133168200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:133166600-133168200	Enhancers	Liver	Liver
21	chr3:133166600-133168400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:133166600-133169400	Enhancers	Thymus	Thymus
23	chr3:133166800-133167400	Flanking Active TSS	GM12878-XiMat	blood
24	chr3:133166800-133167600	Enhancers	Gastric	stomach
25	chr3:133166800-133168000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:133166800-133168000	Enhancers	Stomach Mucosa	stomach
27	chr3:133166800-133168200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:133166800-133168200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:133166800-133168200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:133166800-133168200	Enhancers	Duodenum Mucosa	Duodenum
31	chr3:133166800-133168600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr3:133166800-133171000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:133167000-133167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:133167000-133167800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:133167000-133168200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:133167000-133168200	Enhancers	A549	lung
37	chr3:133167000-133168200	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:133167000-133168400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr3:133167000-133170800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:133167200-133167600	Enhancers	Fetal Brain Male	brain
41	chr3:133167200-133168000	Enhancers	Fetal Brain Female	brain

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