Variant report

Variant	rs9868056
Chromosome Location	chr3:69249770-69249771
allele	G/T
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	chr3:69249659-69250222	HepG2	liver:	n/a	chr3:69249840-69249856 chr3:69249845-69249855
2	FOXA1	chr3:69249766-69250268	HepG2	liver:	n/a	n/a
3	MAZ	chr3:69249541-69250293	HepG2	liver:	n/a	n/a
4	USF2	chr3:69249622-69250298	Hela-S3	cervix:	n/a	n/a
5	JUND	chr3:69249576-69250237	K562	blood:	n/a	chr3:69250044-69250058
6	TEAD4	chr3:69249704-69250230	MCF-7	breast:	n/a	n/a
7	CEBPB	chr3:69249544-69250251	MCF-7	breast:	n/a	n/a
8	TCF12	chr3:69249646-69250330	ECC-1	luminal epithelium:	n/a	n/a
9	CEBPB	chr3:69249599-69249863	A549	lung:	n/a	n/a
10	RCOR1	chr3:69249276-69250328	Hela-S3	cervix:	n/a	n/a
11	JUN	chr3:69249617-69250047	HepG2	liver:	n/a	n/a
12	SP1	chr3:69249498-69250324	A549	lung:	n/a	n/a
13	SMC3	chr3:69249575-69250287	HepG2	liver:	n/a	n/a
14	EP300	chr3:69249683-69250239	HepG2	liver:	n/a	n/a
15	TCF12	chr3:69249646-69250270	MCF-7	breast:	n/a	n/a
16	STAT3	chr3:69249107-69250193	MCF10A-Er-Src	breast:	n/a	chr3:69249823-69249831 chr3:69249821-69249832
17	SP1	chr3:69249550-69250349	HepG2	liver:	n/a	n/a
18	SMC3	chr3:69249516-69250302	Hela-S3	cervix:	n/a	n/a
19	HNF4A	chr3:69249592-69250163	HepG2	liver:	n/a	chr3:69249797-69249810 chr3:69249798-69249810 chr3:69249795-69249813 chr3:69249798-69249810 chr3:69249797-69249812 chr3:69249798-69249810 chr3:69250126-69250134 chr3:69249796-69249811 chr3:69249798-69249811 chr3:69249797-69249812 chr3:69249797-69249812 chr3:69250053-69250061 chr3:69249798-69249810 chr3:69249799-69249811
20	TCF7L2	chr3:69249554-69250195	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:69248478-69250687	MCF10A-Er-Src	breast:	n/a	n/a
22	RFX5	chr3:69249524-69250253	Hela-S3	cervix:	n/a	n/a
23	MXI1	chr3:69249206-69250210	Hela-S3	cervix:	n/a	n/a
24	MAX	chr3:69249546-69250365	MCF-7	breast:	n/a	n/a
25	POLR2A	chr3:69249712-69250420	HUVEC	blood vessel:	n/a	n/a
26	YY1	chr3:69249649-69250127	HCT-116	colon:	n/a	chr3:69249840-69249856 chr3:69249845-69249855
27	HEY1	chr3:69249510-69250288	HepG2	liver:	n/a	n/a
28	MAFK	chr3:69248682-69250278	Hela-S3	cervix:	n/a	chr3:69249246-69249261 chr3:69249849-69249864 chr3:69249728-69249745
29	JUND	chr3:69249574-69250168	HepG2	liver:	n/a	chr3:69250044-69250058
30	POLR2A	chr3:69249525-69250233	HepG2	liver:	n/a	n/a
31	E2F4	chr3:69249619-69249912	MCF10A-Er-Src	breast:	n/a	n/a
32	TCF12	chr3:69249390-69250373	A549	lung:	n/a	n/a
33	TAF1	chr3:69249474-69250291	Hela-S3	cervix:	n/a	n/a
34	MAZ	chr3:69249583-69250238	K562	blood:	n/a	n/a
35	POLR2A	chr3:69248412-69250355	Hela-S3	cervix:	n/a	n/a
36	KAP1	chr3:69249510-69250410	HEK293	kidney:	n/a	n/a
37	CREB1	chr3:69249538-69250339	HepG2	liver:	n/a	n/a
38	SIN3AK20	chr3:69249532-69249851	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr3:69249437-69250353	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr3:69249438-69250379	HepG2	liver:	n/a	n/a
41	STAT3	chr3:69248946-69250100	MCF10A-Er-Src	breast:	n/a	chr3:69249094-69249102 chr3:69249823-69249831 chr3:69249821-69249832
42	EP300	chr3:69249709-69250353	ECC-1	luminal epithelium:	n/a	n/a
43	FOXA1	chr3:69249755-69250201	T-47D	breast:	n/a	n/a
44	GATA3	chr3:69249535-69250281	MCF-7	breast:	n/a	chr3:69250088-69250109
45	ARID3A	chr3:69249635-69250318	HepG2	liver:	n/a	n/a
46	CEBPB	chr3:69249498-69250245	MCF-7	breast:	n/a	n/a
47	TBP	chr3:69249254-69250531	Hela-S3	cervix:	n/a	n/a
48	RAD21	chr3:69249510-69250249	Hela-S3	cervix:	n/a	n/a
49	FOS	chr3:69249538-69250197	MCF10A-Er-Src	breast:	n/a	chr3:69250044-69250058
50	CEBPB	chr3:69249544-69249888	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs34263064	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35461234	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35466234	0.81[EUR][1000 genomes]
rs4075188	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4376041	0.81[CEU][hapmap]
rs6772387	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6776027	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6776243	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6781505	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6781739	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6782869	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6784841	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6785253	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6804872	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6806528	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611476	1.00[CHD][hapmap]
rs7637015	0.84[ASN][1000 genomes]
rs7640502	1.00[CHD][hapmap];1.00[JPT][hapmap]

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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69232000-69275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:69242400-69281600	Weak transcription	Brain Germinal Matrix	brain
3	chr3:69242600-69268800	Weak transcription	Spleen	Spleen
4	chr3:69244000-69264800	Weak transcription	Fetal Brain Female	brain
5	chr3:69244200-69261800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:69246200-69266800	Weak transcription	HSMM	muscle
7	chr3:69247000-69254000	Weak transcription	Fetal Brain Male	brain
8	chr3:69247200-69253200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:69247600-69249800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr3:69247600-69249800	Enhancers	Fetal Heart	heart
11	chr3:69247800-69250000	Active TSS	Placenta	Placenta
12	chr3:69248000-69249800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:69248000-69250000	Active TSS	Liver	Liver
14	chr3:69248000-69250200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr3:69248000-69250200	Active TSS	Hela-S3	cervix
16	chr3:69248200-69250000	Active TSS	Esophagus	oesophagus
17	chr3:69248200-69250200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr3:69248200-69257000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:69248400-69249800	Active TSS	Primary B cells from cord blood	blood
20	chr3:69248400-69249800	Active TSS	Adipose Nuclei	Adipose
21	chr3:69248400-69249800	Active TSS	Fetal Kidney	kidney
22	chr3:69248400-69250000	Active TSS	Fetal Intestine Small	intestine
23	chr3:69248400-69250200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:69248400-69250200	Active TSS	Psoas Muscle	Psoas
25	chr3:69248400-69250200	Active TSS	Rectal Smooth Muscle	rectum
26	chr3:69248400-69250200	Active TSS	A549	lung
27	chr3:69248400-69250400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:69248400-69250400	Active TSS	Right Atrium	heart
29	chr3:69248400-69250400	Flanking Active TSS	HUVEC	blood vessel
30	chr3:69248600-69249800	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr3:69248600-69249800	Bivalent/Poised TSS	HepG2	liver
32	chr3:69248600-69250200	Active TSS	Aorta	Aorta
33	chr3:69248600-69250200	Active TSS	Colonic Mucosa	Colon
34	chr3:69248600-69250200	Active TSS	Fetal Stomach	stomach
35	chr3:69248600-69250200	Active TSS	Ovary	ovary
36	chr3:69248600-69250200	Active TSS	Pancreas	Pancrea
37	chr3:69248600-69250200	Active TSS	Right Ventricle	heart
38	chr3:69248600-69250200	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr3:69248600-69250200	Active TSS	Stomach Mucosa	stomach
40	chr3:69248600-69250200	Active TSS	Stomach Smooth Muscle	stomach
41	chr3:69248600-69250400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:69248800-69250000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr3:69248800-69250200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:69249000-69249800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:69249000-69249800	Enhancers	Brain Hippocampus Middle	brain
46	chr3:69249000-69250000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:69249000-69250200	Active TSS	Fetal Intestine Large	intestine
48	chr3:69249000-69250200	Active TSS	NHDF-Ad	bronchial
49	chr3:69249000-69250400	Enhancers	Brain Cingulate Gyrus	brain
50	chr3:69249000-69250400	Enhancers	Fetal Muscle Leg	muscle

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