Variant report

Variant	rs6776027
Chromosome Location	chr3:69253455-69253456
allele	C/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	MAX	chr3:69253185-69254142	A549	lung:	n/a	chr3:69253361-69253372 chr3:69253240-69253250 chr3:69253360-69253373 chr3:69253362-69253372 chr3:69253362-69253371 chr3:69253361-69253371 chr3:69253363-69253370 chr3:69253362-69253371 chr3:69253361-69253372
2	BCL3	chr3:69253380-69253684	GM12878	blood:	n/a	n/a
3	WRNIP1	chr3:69253294-69254074	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:69252957-69254093	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA3	chr3:69253260-69254241	A549	lung:	n/a	chr3:69253516-69253524 chr3:69253633-69253642
6	ATF2	chr3:69253344-69253849	GM12878	blood:	n/a	n/a
7	FOS	chr3:69253193-69254052	MCF10A-Er-Src	breast:	n/a	chr3:69253587-69253599 chr3:69253630-69253641 chr3:69253631-69253641 chr3:69253633-69253644 chr3:69253631-69253641
8	NFATC1	chr3:69253329-69253821	GM12878	blood:	n/a	n/a
9	NFIC	chr3:69253344-69253854	GM12878	blood:	n/a	n/a
10	IRF4	chr3:69253312-69253684	GM12878	blood:	n/a	n/a
11	FOS	chr3:69253417-69253985	MCF10A-Er-Src	breast:	n/a	chr3:69253587-69253599 chr3:69253630-69253641 chr3:69253631-69253641 chr3:69253633-69253644 chr3:69253631-69253641
12	RUNX3	chr3:69253360-69254046	GM12878	blood:	n/a	n/a
13	IKZF1	chr3:69253040-69253913	GM12878	blood:	n/a	n/a
14	TCF12	chr3:69253316-69254190	A549	lung:	n/a	n/a
15	ATF2	chr3:69253369-69253827	GM12878	blood:	n/a	n/a
16	FOS	chr3:69253371-69253858	HUVEC	blood vessel:	n/a	chr3:69253587-69253599 chr3:69253630-69253641 chr3:69253631-69253641 chr3:69253633-69253644 chr3:69253631-69253641
17	FOXM1	chr3:69253262-69253854	GM12878	blood:	n/a	n/a
18	RELA	chr3:69253081-69254081	GM12891	blood:	n/a	chr3:69253168-69253177 chr3:69253168-69253177
19	EP300	chr3:69253194-69253971	GM12878	blood:	n/a	n/a
20	STAT5A	chr3:69253420-69253786	GM12878	blood:	n/a	n/a
21	FOS	chr3:69252911-69254134	MCF10A-Er-Src	breast:	n/a	chr3:69253587-69253599 chr3:69253630-69253641 chr3:69253631-69253641 chr3:69253633-69253644 chr3:69253631-69253641
22	MTA3	chr3:69253259-69253809	GM12878	blood:	n/a	n/a
23	SP1	chr3:69253309-69254098	A549	lung:	n/a	n/a
24	MYC	chr3:69252957-69254155	MCF10A-Er-Src	breast:	n/a	chr3:69253361-69253372 chr3:69253240-69253250 chr3:69253360-69253373 chr3:69253362-69253372 chr3:69253362-69253371 chr3:69253361-69253371 chr3:69253363-69253370 chr3:69253362-69253371 chr3:69253361-69253372
25	PML	chr3:69253178-69253877	GM12878	blood:	n/a	n/a
26	STAT3	chr3:69253322-69253612	MCF10A-Er-Src	breast:	n/a	n/a
27	NFIC	chr3:69252928-69254016	GM12878	blood:	n/a	n/a
28	STAT3	chr3:69253018-69254151	MCF10A-Er-Src	breast:	n/a	chr3:69253237-69253249
29	STAT3	chr3:69252999-69254167	MCF10A-Er-Src	breast:	n/a	chr3:69253237-69253249
30	BATF	chr3:69253405-69253989	GM12878	blood:	n/a	n/a
31	BCL11A	chr3:69253448-69253667	GM12878	blood:	n/a	n/a
32	BATF	chr3:69253444-69253731	GM12878	blood:	n/a	n/a
33	FOSL2	chr3:69253290-69254156	A549	lung:	n/a	chr3:69253587-69253599 chr3:69253631-69253641 chr3:69253633-69253644 chr3:69253631-69253641
34	STAT3	chr3:69253000-69254020	MCF10A-Er-Src	breast:	n/a	chr3:69253237-69253249
35	JUN	chr3:69253439-69253770	HUVEC	blood vessel:	n/a	chr3:69253587-69253599 chr3:69253631-69253641 chr3:69253633-69253644 chr3:69253631-69253641
36	ZNF143	chr3:69253315-69254030	GM12878	blood:	n/a	n/a
37	E2F4	chr3:69253402-69254003	MCF10A-Er-Src	breast:	n/a	n/a
38	MYC	chr3:69253150-69254035	MCF10A-Er-Src	breast:	n/a	chr3:69253361-69253372 chr3:69253240-69253250 chr3:69253360-69253373 chr3:69253362-69253372 chr3:69253362-69253371 chr3:69253361-69253371 chr3:69253363-69253370 chr3:69253362-69253371 chr3:69253361-69253372
39	BCL11A	chr3:69253399-69253773	GM12878	blood:	n/a	n/a
40	FOS	chr3:69252960-69254094	MCF10A-Er-Src	breast:	n/a	chr3:69253587-69253599 chr3:69253630-69253641 chr3:69253631-69253641 chr3:69253633-69253644 chr3:69253631-69253641
41	EBF1	chr3:69252905-69254063	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs34263064	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34416281	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34511838	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35423263	0.85[AMR][1000 genomes]
rs35461234	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35466234	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35530977	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35860408	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36022055	0.85[AMR][1000 genomes]
rs4075188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376041	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4582065	0.85[AMR][1000 genomes]
rs4621334	0.85[AMR][1000 genomes]
rs6772387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776243	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782869	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6784841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785253	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804872	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6806528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73097720	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73097725	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73097726	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73097740	0.85[AMR][1000 genomes]
rs7637015	0.92[ASN][1000 genomes]
rs7640502	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9868056	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[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:78 , 50 per page) page: 1 2

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	chr3:69248200-69257000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:69249000-69255400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr3:69249000-69263000	Weak transcription	Lung	lung
11	chr3:69249400-69257600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:69249800-69254600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:69249800-69254600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:69250000-69253600	Weak transcription	HSMMtube	muscle
15	chr3:69250000-69255200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr3:69250000-69258400	Weak transcription	Fetal Thymus	thymus
17	chr3:69250000-69261600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:69250000-69263000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:69250000-69269200	Weak transcription	Thymus	Thymus
20	chr3:69250000-69272400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:69250000-69281600	Weak transcription	Esophagus	oesophagus
22	chr3:69250200-69254800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:69250200-69255400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:69250200-69255600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:69250200-69257600	Weak transcription	Fetal Lung	lung
26	chr3:69250200-69262000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:69250200-69262800	Weak transcription	Fetal Stomach	stomach
28	chr3:69250200-69263200	Weak transcription	Dnd41	blood
29	chr3:69250200-69268800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:69250200-69268800	Weak transcription	Ovary	ovary
31	chr3:69250200-69286000	Weak transcription	Colonic Mucosa	Colon
32	chr3:69250400-69254800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:69250400-69260200	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:69250400-69264800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:69250400-69268400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:69250400-69280000	Weak transcription	Fetal Kidney	kidney
37	chr3:69251800-69254200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:69252600-69253600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:69252600-69253600	Enhancers	Brain Anterior Caudate	brain
40	chr3:69252600-69254000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr3:69252600-69254000	Enhancers	Brain Cingulate Gyrus	brain
42	chr3:69252600-69254000	Enhancers	Brain Hippocampus Middle	brain
43	chr3:69252600-69254000	Enhancers	Brain Substantia Nigra	brain
44	chr3:69252600-69254000	Enhancers	Fetal Intestine Large	intestine
45	chr3:69252600-69254000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:69252600-69254000	Flanking Active TSS	NHEK	skin
47	chr3:69252600-69254200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:69252600-69254200	Enhancers	Brain Angular Gyrus	brain
49	chr3:69252600-69254200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr3:69252600-69254600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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