Variant report

Variant	rs3755819
Chromosome Location	chr3:48595419-48595420
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	CTCF	chr3:48595414-48596180	A549	lung:	n/a	chr3:48595794-48595807 chr3:48595765-48595781 chr3:48595759-48595780
2	POLR2A	chr3:48595372-48595878	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48593999-48595944	Raji	blood:	n/a	n/a
4	POLR2A	chr3:48593228-48597216	U87	brain:	n/a	n/a
5	E2F4	chr3:48595210-48595901	MCF10A-Er-Src	breast:	n/a	chr3:48595672-48595679 chr3:48595671-48595683 chr3:48595672-48595679 chr3:48595671-48595680 chr3:48595670-48595681 chr3:48595672-48595679
6	TBP	chr3:48595197-48595880	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD1	chr3:48595381-48596055	IMR90	lung:	n/a	n/a
8	TBP	chr3:48595182-48595853	GM12878	blood:	n/a	n/a
9	MXI1	chr3:48593292-48599174	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr3:48595267-48596179	HCT-116	colon:	n/a	chr3:48595762-48595781 chr3:48595564-48595573 chr3:48595764-48595776
11	CTCF	chr3:48595337-48596196	HCT-116	colon:	n/a	chr3:48595794-48595807 chr3:48595765-48595781 chr3:48595759-48595780
12	HA-E2F1	chr3:48595377-48595916	MCF-7	breast:	n/a	chr3:48595672-48595679 chr3:48595671-48595683 chr3:48595672-48595679 chr3:48595671-48595680 chr3:48595672-48595679
13	NFIC	chr3:48595415-48595997	ECC-1	luminal epithelium:	n/a	chr3:48595981-48595997
14	CTCF	chr3:48595413-48596218	SK-N-SH	brain:	n/a	chr3:48595794-48595807 chr3:48595765-48595781 chr3:48595759-48595780
15	MAZ	chr3:48595407-48596126	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:48588992-48602017	U87	brain:	n/a	n/a
17	CHD1	chr3:48595264-48595807	H1-hESC	embryonic stem cell:	n/a	n/a
18	MYBL2	chr3:48595404-48595971	HepG2	liver:	n/a	n/a
19	RCOR1	chr3:48595403-48596452	IMR90	lung:	n/a	n/a
20	GTF3C2	chr3:48594540-48595795	K562	blood:	n/a	n/a
21	MAZ	chr3:48595322-48595936	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:48593253-48597224	U87	brain:	n/a	n/a
23	POLR2A	chr3:48595407-48595955	HCT-116	colon:	n/a	n/a
24	POLR2A	chr3:48595402-48596002	HepG2	liver:	n/a	n/a
25	POLR2A	chr3:48592306-48602182	U87	brain:	n/a	n/a
26	POLR2A	chr3:48593734-48595877	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr3:48595393-48595822	K562	blood:	n/a	n/a
28	PML	chr3:48595371-48596145	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:48594090-48595871	GM12878	blood:	n/a	n/a
30	MYBL2	chr3:48595363-48595969	HepG2	liver:	n/a	n/a
31	TBP	chr3:48595108-48595896	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48593498..48596370-chr3:48671883..48674161,2	K562	blood:
2	chr3:48487725..48489433-chr3:48594364..48597196,2	MCF-7	breast:
3	chr3:48594247..48597141-chr3:48671392..48674077,2	MCF-7	breast:
4	chr3:48505137..48507791-chr3:48593397..48596225,2	K562	blood:
5	chr3:48486334..48488063-chr3:48594171..48595954,2	MCF-7	breast:
6	chr3:48484123..48488497-chr3:48591865..48597132,6	K562	blood:
7	chr3:48512815..48516100-chr3:48594601..48597600,3	K562	blood:
8	chr3:48507541..48509747-chr3:48593128..48595485,2	MCF-7	breast:
9	chr3:48593030..48597118-chr3:48698507..48702121,6	MCF-7	breast:
10	chr3:48510260..48512404-chr3:48592890..48595693,2	MCF-7	breast:
11	chr3:48507211..48510003-chr3:48593897..48596885,2	MCF-7	breast:
12	chr3:48592800..48598084-chr3:48598125..48603493,9	MCF-7	breast:
13	chr3:48595330..48596067-chr3:48723057..48723813,2	MCF-7	breast:
14	chr3:48592861..48595715-chr3:48598424..48603731,6	K562	blood:
15	chr3:48593859..48595612-chr3:48717016..48718760,2	MCF-7	breast:
16	chr3:48594740..48597217-chr3:48645674..48647413,2	MCF-7	breast:
17	chr3:48591611..48596652-chr3:48640512..48642956,4	MCF-7	breast:
18	chr3:48595024..48597915-chr3:48619806..48622273,2	K562	blood:
19	chr3:48594423..48596370-chr3:48671883..48674168,2	K562	blood:

Variant related genes	Relation type
PFKFB4	TF binding region
ENSG00000225697	Chromatin interaction
ENSG00000145040	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000164053	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10470687	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060933	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091944	0.94[ASN][1000 genomes]
rs13094578	0.82[ASN][1000 genomes]
rs13100178	0.82[ASN][1000 genomes]
rs13319635	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13319651	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17080289	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2006871	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2854394	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2854395	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28563843	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28581474	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35343040	0.85[ASN][1000 genomes]
rs35562294	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35796820	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3969942	0.82[ASN][1000 genomes]
rs4075082	0.82[ASN][1000 genomes]
rs6442127	0.81[ASN][1000 genomes]
rs6781283	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792156	0.86[ASN][1000 genomes]
rs6792525	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806059	0.94[ASN][1000 genomes]
rs7428949	0.82[ASN][1000 genomes]
rs7434077	0.82[ASN][1000 genomes]
rs7434107	0.82[ASN][1000 genomes]
rs7623614	0.82[ASN][1000 genomes]
rs7640031	0.82[ASN][1000 genomes]
rs7644771	0.82[ASN][1000 genomes]
rs9810549	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9810991	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814951	0.85[EUR][1000 genomes]
rs9816942	0.82[ASN][1000 genomes]
rs9830581	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9835902	0.81[ASN][1000 genomes]
rs9837687	0.95[ASN][1000 genomes]
rs9843316	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848824	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9849280	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850102	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851743	0.82[ASN][1000 genomes]
rs9851771	0.82[ASN][1000 genomes]
rs9864729	0.95[ASN][1000 genomes]
rs9869698	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871180	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871608	0.82[ASN][1000 genomes]
rs9878950	0.98[ASN][1000 genomes]
rs9881877	0.97[ASN][1000 genomes]
rs9882962	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48593400-48595600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr3:48593600-48595600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr3:48593600-48599000	Enhancers	Stomach Mucosa	stomach
4	chr3:48593800-48595600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr3:48594200-48595800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:48594400-48595800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:48594600-48595600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr3:48594600-48595600	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr3:48594600-48595600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:48594600-48595600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:48594600-48595600	Flanking Active TSS	Osteobl	bone
12	chr3:48594600-48595800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr3:48594600-48595800	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr3:48594600-48595800	Flanking Active TSS	Dnd41	blood
15	chr3:48594600-48596800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr3:48594600-48599200	Enhancers	Fetal Heart	heart
17	chr3:48594600-48599200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:48594800-48595800	Weak transcription	HSMMtube	muscle
19	chr3:48594800-48597400	Weak transcription	Lung	lung
20	chr3:48594800-48597600	Weak transcription	Gastric	stomach
21	chr3:48595000-48595600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:48595000-48595600	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr3:48595000-48595600	Weak transcription	HSMM	muscle
24	chr3:48595000-48595600	Enhancers	HUVEC	blood vessel
25	chr3:48595000-48595800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:48595000-48595800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:48595000-48595800	Enhancers	Adipose Nuclei	Adipose
28	chr3:48595000-48596000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:48595000-48596000	Enhancers	Fetal Lung	lung
30	chr3:48595000-48596200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:48595000-48596200	Enhancers	Liver	Liver
32	chr3:48595000-48596200	Enhancers	NHLF	lung
33	chr3:48595000-48596400	Weak transcription	Brain Angular Gyrus	brain
34	chr3:48595000-48596400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:48595000-48596600	Enhancers	A549	lung
36	chr3:48595000-48597000	Weak transcription	Psoas Muscle	Psoas
37	chr3:48595000-48597400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:48595000-48597400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:48595000-48597400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:48595000-48597400	Weak transcription	Fetal Kidney	kidney
41	chr3:48595000-48597400	Weak transcription	Left Ventricle	heart
42	chr3:48595000-48597400	Weak transcription	Ovary	ovary
43	chr3:48595000-48597400	Weak transcription	Right Atrium	heart
44	chr3:48595000-48597600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:48595000-48597600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:48595000-48597600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr3:48595000-48597800	Enhancers	NHDF-Ad	bronchial
48	chr3:48595000-48598000	Enhancers	Primary hematopoietic stem cells	blood
49	chr3:48595000-48598000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:48595000-48598000	Enhancers	Placenta	Placenta

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