Variant report

Variant	rs9875511
Chromosome Location	chr3:69248608-69248609
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	MYC	chr3:69248536-69248704	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr3:69248476-69248622	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:69248478-69250687	MCF10A-Er-Src	breast:	n/a	n/a
4	EBF1	chr3:69248526-69248845	GM12878	blood:	n/a	n/a
5	RUNX3	chr3:69248543-69248844	GM12878	blood:	n/a	n/a
6	SPI1	chr3:69248562-69248955	HL-60	blood:	n/a	n/a
7	STAT3	chr3:69248471-69248849	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr3:69248412-69250355	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr3:69248500-69248772	MCF10A-Er-Src	breast:	n/a	n/a
10	EBF1	chr3:69248591-69248845	GM12878	blood:	n/a	n/a
11	MTA3	chr3:69248476-69248888	GM12878	blood:	n/a	n/a
12	IRF1	chr3:69248520-69248834	K562	blood:	n/a	chr3:69248648-69248661 chr3:69248652-69248666 chr3:69248651-69248662 chr3:69248650-69248661 chr3:69248655-69248672 chr3:69248650-69248664
13	NFIC	chr3:69248423-69248995	GM12878	blood:	n/a	n/a
14	EBF1	chr3:69248566-69248919	GM12878	blood:	n/a	n/a
15	PRDM1	chr3:69248512-69248791	Hela-S3	cervix:	n/a	chr3:69248653-69248662 chr3:69248648-69248663 chr3:69248649-69248663 chr3:69248649-69248662
16	IRF1	chr3:69248486-69248844	K562	blood:	n/a	chr3:69248648-69248661 chr3:69248652-69248666 chr3:69248651-69248662 chr3:69248650-69248661 chr3:69248655-69248672 chr3:69248650-69248664
17	SPI1	chr3:69248568-69248856	GM12891	blood:	n/a	n/a
18	STAT3	chr3:69248451-69248619	MCF10A-Er-Src	breast:	n/a	n/a
19	RUNX3	chr3:69248451-69248949	GM12878	blood:	n/a	n/a
20	ARID3A	chr3:69248519-69248954	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11128118	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11712024	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12172924	0.97[ASN][1000 genomes]
rs12637416	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13059488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13059687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13082480	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs28529735	0.83[ASN][1000 genomes]
rs4358306	0.90[ASN][1000 genomes]
rs4464459	0.81[ASN][1000 genomes]
rs4473559	0.81[ASN][1000 genomes]
rs4493438	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4508787	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4541413	0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4624565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67268350	0.88[ASN][1000 genomes]
rs6763046	0.82[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6765197	0.85[ASN][1000 genomes]
rs6765309	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6777671	0.86[CEU][hapmap]
rs6804718	0.86[ASN][1000 genomes]
rs7647940	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs9310140	0.81[ASN][1000 genomes]
rs9831516	0.88[JPT][hapmap]
rs9833167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9836305	0.88[JPT][hapmap]
rs9838728	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9847983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9853318	0.87[ASN][1000 genomes]
rs9853587	0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9853744	0.86[ASN][1000 genomes]
rs9860235	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9872199	0.88[JPT][hapmap]
rs9872489	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3398378	chr3:69240573-69271936	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69231400-69249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:69231800-69249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:69232000-69248800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:69232000-69249400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:69232000-69275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:69232800-69249200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:69242400-69281600	Weak transcription	Brain Germinal Matrix	brain
8	chr3:69242600-69249400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:69242600-69268800	Weak transcription	Spleen	Spleen
10	chr3:69244000-69264800	Weak transcription	Fetal Brain Female	brain
11	chr3:69244200-69261800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:69244600-69249400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:69246200-69249600	Weak transcription	HSMMtube	muscle
14	chr3:69246200-69266800	Weak transcription	HSMM	muscle
15	chr3:69246400-69249600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:69246400-69249600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:69246600-69249600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:69246600-69249600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:69246600-69249600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:69247000-69249600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:69247000-69249600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:69247000-69249600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr3:69247000-69254000	Weak transcription	Fetal Brain Male	brain
24	chr3:69247200-69253200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:69247600-69249600	Active TSS	Duodenum Mucosa	Duodenum
26	chr3:69247600-69249800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr3:69247600-69249800	Enhancers	Fetal Heart	heart
28	chr3:69247800-69249600	Weak transcription	Fetal Lung	lung
29	chr3:69247800-69249600	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr3:69247800-69250000	Active TSS	Placenta	Placenta
31	chr3:69248000-69248800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:69248000-69248800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr3:69248000-69249400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:69248000-69249800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:69248000-69250000	Active TSS	Liver	Liver
36	chr3:69248000-69250200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr3:69248000-69250200	Active TSS	Hela-S3	cervix
38	chr3:69248200-69249000	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr3:69248200-69249400	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr3:69248200-69249600	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr3:69248200-69249600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:69248200-69250000	Active TSS	Esophagus	oesophagus
43	chr3:69248200-69250200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr3:69248200-69257000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:69248400-69248800	Active TSS	Muscle Satellite Cultured Cells	--
46	chr3:69248400-69248800	Active TSS	Brain Anterior Caudate	brain
47	chr3:69248400-69248800	Active TSS	Thymus	Thymus
48	chr3:69248400-69248800	Active TSS	GM12878-XiMat	blood
49	chr3:69248400-69249000	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr3:69248400-69249000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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